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2024-03-29T14:49:15Z
User contributions
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https://wiki.tanakalab.org/index.php?title=Letter_to_Froppier_(French)&diff=607
Letter to Froppier (French)
2015-02-02T09:48:53Z
<p>Serghein: </p>
<hr />
<div>{|-<br />
| <ul style="text-align: left; list-style: none; margin-left: 0px"><br />
<li>G. FROPPIER</li><br />
<li>Responsable Scientifique</li><br />
<li>Elevage Scientifique des Dombes</li><br />
<li>Tél : 04 74 55 34 97</li><br />
<li>Fax : 04 74 55 10 32</li><br />
<li>Email : gfr@esdfrance.com</li><br />
</ul><br />
| <ul style="text-align: left; list-style: none; margin-left: 500px"><br />
<li>Max-Planck Institute</li> <br />
<li>Of Molecular Cell Biology and Genetics</li> <br />
<li>Pfotenhauerstrasse 108</li> <br />
<li>01307 Dresden</li> <br />
<li>GERMANY</li> <br />
</ul><br />
|}<br />
<br />
<ul style="text-align: left; list-style: none; margin-left: 500px"><br />
<li>Dresden, le 22.07.03</li><br />
</ul><br />
<br />
Cher Monsieur,<br />
<br />
Vous trouverez ci-joint les 2 antigenes suivants:<br />
<br />
Msx1-M0412 (0.81 mg/ml)<br />
<br />
Msx1-M0421 (0.63 mg/ml)<br />
<br />
Il y a 5 tubes par antigene. Le tube avec le point rouge est destine a l’injection primaire et les tubes avec les points noirs sont destines aux boosts. <br />
<br />
Nous vous prions de suivre le meme protocol utilise pour Madame Oegema de Max-Planck Institute CBG.<br />
<br />
<br />
Je vous prie de croire, monsieur, en l’expression de mes sentiments distingues.</div>
Serghein
https://wiki.tanakalab.org/index.php?title=Overview&diff=306
Overview
2014-03-04T11:19:20Z
<p>Serghein: /* Molecular biology */</p>
<hr />
<div>== Introduction ==<br />
On the pages listed below you can find most common protocols used in the lab as well as a list of lab duties along with the names of the responsible persons. Please, contact the responsible persons if you have any question, suggestions or troubles.<br />
<br />
== Axolotl ==<br />
<br />
=== Maintainance ===<br />
In this section you will find some general information on how to [[Axolotl#Maintaining_the_axolotls|maintain]] the animals.<br />
<br />
=== Feeding ===<br />
This section will give you an overview of how to [[Axolotl#Feeding|feed]] the axolotls.<br />
<br />
=== Interesting observations ===<br />
In the following section you can find some [[Axolotl#Interesting_observations|interesting observations]] concerning the axolotl, its behavior, caveats of the transgenics and many more.<br />
<br />
== Lab duties ==<br />
<ul><br />
=== Chemicals ===<br />
<li>[[Antibiotics|Antibiotics]]</li><br />
<li>[[Benzocaine|Benzocaine]]</li><br />
<li>[[Fibronectin|Fibronectin]]</li><br />
<li>[[Gelatine|Gelatine]]</li><br />
<li>[[Liquid_nitrogen|Liquid nitrogen]]</li><br />
<li>[[Primary_antibodies|Primary antibodies]]</li><br />
<li>[[Secondary_antibodies|Secondary antibodies]]</li><br />
<li>[[Serum_heat_inactivation|Serum heat inactivation]]</li><br />
<br />
=== Hardware ===<br />
<li>[[Autoclave|Autoclave]]</li><br />
<li>[[Cryostat|Cryostat]]</li><br />
<li>[[Dissecting_microscopes|Dissecting microscopes]]</li><br />
<li>[[Leica_confocal_microscope|Leica confocal microscope]]</li><br />
<li>[[Vacuum_pumps|Vacuum pumps]]</li><br />
<li>[[Waterbath|Waterbath]]</li><br />
<br />
=== General ===<br />
<li>[[Ordering_common_stuff|Ordering common stuff]]</li><br />
<li>[[Heat_shock_competent_cells|Heat-shock competent cells]]</li><br />
</ul><br />
<br />
<br />
== Protocols ==<br />
<ul><br />
=== Cell culture ===<br />
<li>[[Blastema_cells|Blastema cells]]</li><br />
<li>[[Baculovirus_titration|Baculovirus titration]]</li><br />
<li>[[Myoblasts_electroporation|Myoblasts electroporation]]</li><br />
<li>[[Adhesive_cell_culture|Adhesive cell culture]]</li><br />
<li>[[Electroporation_of_blastema_cells|Electroporation of blastema cells]]</li><br />
<li>[[Electroporation_of_nec|Electroporation of neural epithelia cells (axolotl spinal cord)]]</li><br />
<li>[[mESC_culture|mESC culture/Cyst formation]]</li><br />
<li>[[Neurosphere_culture|Neurosphere culture]]</li><br />
=== Histology ===<br />
<li>[[Double_Immunostaining_via_antigen_retrieval|Double Immunostaining via antigen retrieval (Sherry)]]</li><br />
=== Molecular biology ===<br />
<li>[[Metamorphosis_protocol|Metamorphosis protocol (Sherry)]]</li><br />
<li>[[Digestion_DNA|Digestion (Plasmid DNA)]]</li><br />
</ul><br />
<br />
== Lab business ==<br />
=== Ordering database ===<br />
Use the following [http://ordering-db.biotec.tu-dresden.de/ordering/login.gsp ordering database] to place your orders.<br />
<br />
=== Booking calendars ===<br />
Since some pieces of hardware are used intensively it is necessary to book them in advance. The links to the corresponding booking calendars are listed below.<br />
<ul><br />
<li><br />
Fluorescence microscopes<br />
<ul><br />
<li>[http://www.my.calendars.net/olympusszx16 Olympus SZX 16]</li><br />
<li>[http://www.my.calendars.net/new_olympus/ New Olympus SZX 16]</li><br />
<li>[http://www.my.calendars.net/Olympus_OVK Olympus OVK]</li><br />
<li>[http://www.my.calendars.net/axio_observer/ Axio Observer]</li><br />
</ul><br />
</li><br />
<li><br />
Microinjectors and electroporators and dissecting microscope<br />
<ul><br />
<li>Room 0.232<br />
<ul> <br />
<li>[http://www.my.calendars.net/electroporator Nepa Gene]</li><br />
<li>[http://www.my.calendars.net/electroporator2 ECM 830]</li><br />
<li>[http://www.my.calendars.net/stereoscope2/d01/11/2012 Olympus dissecting microscope]</li><br />
</ul><br />
</li><br />
<li>Lab<br />
<ul><br />
<li>[http://www.my.calendars.net/OlympusLab Olympus (next to the axolotls)]</li><br />
<li>[http://www.my.calendars.net/OlympusLab2 Olympus (next to the Microtome)]</li><br />
</ul><br />
</li><br />
</ul><br />
</li><br />
<li><br />
Confocal microscopes<br />
<ul><br />
<li>[http://www.my.calendars.net/leica_lsm Leica LSM]</li><br />
</ul><br />
</li><br />
<li><br />
Cryostats<br />
<ul><br />
<li>[http://www.my.calendars.net/cryostat1 Cryostat 1]</li><br />
<li>[http://www.my.calendars.net/cryostat2 Cryostat 2]</li><br />
</ul><br />
</li><br />
<li><br />
Microtome<br />
<ul><br />
<li>[http://www.my.calendars.net/microtome Microtome]</li><br />
</ul><br />
</li><br />
<li><br />
Paraffin embedding station<br />
<ul><br />
<li>[http://www.my.calendars.net/wax_station Paraffin embedding station]</li><br />
</ul><br />
</li><br />
</ul><br />
<br />
== Genetics ==<br />
=== Transgenic lines ===<br />
<ul><br />
<li>[[Transgenic_axolotl_lines|Axolotl (A.mexicanum)]]</li><br />
<li>[[Transgenic_frog_lines|Frog (X.laevis)]]</li><br />
</ul><br />
<br />
=== Markers ===<br />
{| class="wikitable sortable"<br />
!style="width: 150px" | Marker<br />
!style="width: 250px" | Full name<br />
!style="width: 250px" | Target<br />
!style="width: 450px" | Remarks<br />
!style="width: 200px" | Link<br />
|-<br />
|DAPI/Hoechst<br />
|4',6-diamidino-2-phenylindole<br />
|Nuclei<br />
|Incorporates into the DNA<br />
|[http://en.wikipedia.org/wiki/DAPI DAPI], [http://en.wikipedia.org/wiki/Hoechst_stain Hoechst]<br />
|-<br />
|PCNA<br />
|Proliferating-Cell-Nuclear-Antigen<br />
|Dividing cells<br />
|<br />
|[http://en.wikipedia.org/wiki/PCNA PCNA]<br />
|-<br />
|SOX2<br />
|SRY (sex determining region Y)-box 2<br />
|Preferentially neuronal lineage<br />
|Progenitor marker for both spinal cord and brain<br />
|[http://en.wikipedia.org/wiki/Sox2 SOX2]<br />
|-<br />
|PAX6<br />
|Paired box protein Pax-6<br />
|Brain/spinal cord<br />
|aka aniridia type II protein (AN2) or oculorhombin<br />
|[http://en.wikipedia.org/wiki/Pax6 PAX6]<br />
|-<br />
|PAX7<br />
|Paired box protein Pax-7<br />
|Satellite cells/spinal cord/brain<br />
|<br />
|[http://en.wikipedia.org/wiki/PAX7 PAX7]<br />
|-<br />
|MHC<br />
|Myosin heavy chain<br />
|Muscle fibers<br />
|<br />
|[http://en.wikipedia.org/wiki/Myosin_heavy_chain MHC]<br />
|-<br />
|MYF5<br />
|Myogenic factor 5<br />
|Myoblasts<br />
|Regulates muscle differentiation, labels cycling myoblasts<br />
|[http://en.wikipedia.org/wiki/Myf5 MYF5]<br />
|-<br />
|TUBB3<br />
|ßIII-tubulin<br />
|Axons<br />
|<br />
|[http://en.wikipedia.org/wiki/TUBB3 TUBB3]<br />
|-<br />
|MBP<br />
|Myelin basic protein<br />
|Schwann cells<br />
|<br />
|-<br />
|PRRX1<br />
|Paired mesoderm homeobox protein 1<br />
|Connective tissue progenitors in Limb bud and Limb Blastema<br />
|<br />
|[http://en.wikipedia.org/wiki/PRRX1 PRRX1]<br />
|-<br />
|SMA<br />
|Smooth muscle actin<br />
|Blood vessels/endothelial cells<br />
|<br />
|<br />
|-<br />
|GFAP<br />
|Glial fibrillary acidic protein<br />
|Glia<br />
|<br />
|[http://en.wikipedia.org/wiki/Glial_fibrillary_acidic_protein GFAP]<br />
|-<br />
|NeuN<br />
|Feminizing Locus on X-3, Fox-3, or Hexaribonucleotide Binding Protein-3<br />
|Differentiated nerve<br />
|<br />
|[http://en.wikipedia.org/wiki/NeuN NeuN]<br />
|-<br />
|LEU7/HNK1/B3GAT1/CD57<br />
|Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 1<br />
|Schwann cells<br />
|<br />
|[http://en.wikipedia.org/wiki/B3GAT1 B3GAT1]<br />
|-<br />
|XBRA<br />
|Xbrachyury<br />
|Mesoderm during gastrula stage<br />
|<br />
|[http://en.wikipedia.org/wiki/Brachyury Brachyury]<br />
|-<br />
|MSX1<br />
|Muscle segment homeobox, Msh homeobox 1<br />
|Undifferentiated cells<br />
|Transcriptional repressor during embryogenesis<br />
|[http://en.wikipedia.org/wiki/MSX1 MSX1]<br />
|-<br />
|Trypan blue<br />
|<br />
|Dead tissues or cells<br />
|Vital stain<br />
|[http://en.wikipedia.org/wiki/Trypan_blue Trypan blue]<br />
|-<br />
|MEF2C<br />
|Myocyte-specific enhancer factor 2C<br />
|Differentiated muscle cells<br />
|aka MADS box transcription enhancer factor 2, polypeptide C<br />
|[http://en.wikipedia.org/wiki/Mef2c MEF2C]<br />
|-<br />
|PH3<br />
|Phospho-Histone H3<br />
|Mitotic cells<br />
|<br />
|<br />
|-<br />
|BrdU<br />
|Bromodeoxyuridine<br />
|Cells in S-phase<br />
|<br />
|[http://en.wikipedia.org/wiki/Brdu BrdU]<br />
|-<br />
|CASP3<br />
|Caspase 3<br />
|Dying cells<br />
|<br />
|[http://en.wikipedia.org/wiki/CASP3 CASP3]<br />
|-<br />
|GDF5<br />
|Growth/differentiation factor 5<br />
|Joints<br />
|Joint development marker<br />
|[http://en.wikipedia.org/wiki/GDF5 GDF5]<br />
|-<br />
|Survivin<br />
|<br />
|Cleavage furrow<br />
|aka baculoviral inhibitor of apoptosis repeat-containing 5 or BIRC5<br />
|[http://en.wikipedia.org/wiki/Survivin Survivin]<br />
|-<br />
|MAP2<br />
|Microtubule-associated protein 2<br />
|Neurons<br />
|<br />
|[http://en.wikipedia.org/wiki/MAP2 MAP2]<br />
|-<br />
|SOX9<br />
|SRY (sex determining region Y)-box 2<br />
|Cartillage progenitors<br />
|<br />
|[http://en.wikipedia.org/wiki/Sox9 SOX9]<br />
|-<br />
|MBP<br />
|Myelin basic protein<br />
|Myelin sheath<br />
|<br />
|[http://en.wikipedia.org/wiki/Myelin_basic_protein MBP]<br />
|}<br />
<br />
== Digital data ==<br />
Over the years the members of the lab have produced a lot of different data: Sanger sequences, EST libraries, images and so on. <br />
Select a category from the list below in order to view or download the data.<br />
<br />
=== Fileservers ===<br />
{| class="wikitable"<br />
!style="width: 350px" | Location<br />
!style="width: 250px" | Volume size<br />
!style="width: 350px" | Description<br />
!style="width: 350px" | Access<br />
!style="width: 350px" | Location (console only)<br />
|-<br />
|//biodata/groups/<b>crtd_tanaka</b><br />
|16 TB<br />
|General purpose storage space<br />
|Entire Tanaka lab<br />
|<i>biocluster:</i> <b>/group/crtd_tanaka</b><br />
|-<br />
|//biodata/groups/<b>tanaka-ests</b><br />
|247 GB<br />
|EST sequences<br />
|Entire Tanaka lab<br />
|<i>biocluster:</i> <b>/group/tanaka-ests</b><br />
|-<br />
|//biodata/groups/<b>axolotl-transcriptome</b><br />
|500 GB<br />
|Axolotl transcriptome data<br />
|Elly, Sergej<br />
|<i>biocluster:</i> <b>/projects/axolotl-transcriptome</b><br />
|-<br />
|//biodata/groups/<b>tanaka-saori</b><br />
|878 GB<br />
|Special directory for Saori's data<br />
|Elly, Saori, Sergej<br />
|<i>biocluster:</i> <b>/group/tanaka-saori</b><br />
|}<br />
<br />
{{Tip|The path is different, when accessing the file server from the console.}}<br />
<br />
=== Literature ===<br />
<ul><br />
<li>[[Literature#Theses|Theses]]</li><br />
<li>[[Literature#Publications|Publications]]</li><br />
</ul><br />
<br />
=== Databases ===<br />
<ul><br />
<li>[http://elbrus.biochem.mpg.de/ Axolotl transcriptome] website contains the Axolotl transcriptome assemblies</li><br />
<li>[http://newtomics.mpi-bn.mpg.de/ Newt transcriptome] website contains the Newt transcriptome assembly</li><br />
<li>[http://sandberg.cmb.ki.se/redspottednewt/ Red spotted newt transcriptome] website contains the red spotted newt transcriptome assembly</li><br />
<li>[https://python-srv1.mpi-cbg.de/axolotl/cgi-bin/login.cgi Axolotl EST] database contains several ESTs and also some additional information, e.g. the position of the well with the corresponding insert in the Blastema (BL) or Neural tube (NT) library.</li><br />
<li>[http://python-srv1.mpi-cbg.de/axolotl/cgi-bin/login.cgi?dispatch=contig_search.cgi Short insert cDNA library]</li><br />
<li>CURRENTLY UNAVAILABLE! [http://est.age.mpg.de/ Axologle] database contains expression profiling data of Axolotl limb regeneration</li><br />
<li>CURRENTLY UNAVAILABLE! [http://est.age.mpg.de/blast/blast.html Axolotl BLAST] database contains several different BLAST-able Axolotl transciptome assemblies</li><br />
</ul><br />
<br />
=== Datasets ===<br />
<ul><br />
<li>[[Datasets#Sequences|Sequences]]<br />
<ul><br />
<li>[[Datasets#Illumina|Illumina]]</li><br />
<li>[[Datasets#Sanger|Sanger]]</li><br />
<li>[[Datasets#Roche.2F454|Roche/454]]</li><br />
</ul><br />
</li><br />
<li>[[Datasets#Microarrays|Microarrays]]<br />
</ul><br />
<br />
=== Interesting links ===<br />
<ul><br />
<li>[http://www.nytimes.com/video/2013/02/27/science/100000002087758/finding-the-visible-in-the-invisible.html Visible in the invisible]: a movie introducing a new image processing ana analysis technique developed at the MIT.</li><br />
</ul><br />
<br />
== Lab life ==<br />
<ul><br />
<li>[[Lab_photos|Lab photos]]</li><br />
<li>Further pictures can be found in <b>/biodata/groups/crtd_tanaka/LabFun/</b></li><br />
<li>The recepies for Heino's farewell present can be found under <b>/biodata/groups/crtd_tanaka/LabFun/Heino's farewell present/</b></li><br />
<li>The video of the visit of the EU commissioner can be found under <b>/biodata/groups/crtd_tanaka/LabFun/</b></li><br />
</ul></div>
Serghein
https://wiki.tanakalab.org/index.php?title=Digestion_DNA&diff=305
Digestion DNA
2014-03-04T11:17:48Z
<p>Serghein: </p>
<hr />
<div>This enzymatic technique can be used for cleaving DNA molecules at specific sites, ensuring that all DNA fragments that contain a particular sequence have the same size; furthermore, each fragment that contains the desired sequence has the sequence located at exactly the same position within the fragment. The cleavage method makes use of an important class of DNA-cleaving enzymes isolated primarily from bacteria. These enzymes are called restriction endonucleases or restriction enzymes, and they are able to cleave DNA molecules at the positions at which particular short sequences of bases are present.<br />
<br />
<h3>A. Digestion</h3><br />
Total amount of plasmid DNA: ~10µg (less is also possible).<br />
Add:<br />
<ul><br />
<li>10µl enzyme buffer</li><br />
<li>Enzyme: Unit ==>1 U digest 1µg in 1h at 37°C (~ 2 μl enzyme)</li><br />
<li>1 μl BSA (check manuals instructions of the enzyme if it’s necessary or not!)</li><br />
<li>Fill up the reaction volume to 100 μl with dd water</li><br />
<li><b>2-3 hours restriction at 37°C </b></li><br />
</ul><br />
<br />
<br />
<h3>References</h3><br />
<ul><br />
<li><i>Hartl, Daniel L., Jones, Elizabeth W. (2001), Genetics: Analysis of Genes and Genomes, Fifth Edition</i></li><br />
</ul></div>
Serghein
https://wiki.tanakalab.org/index.php?title=Digestion_DNA&diff=304
Digestion DNA
2014-03-04T11:13:30Z
<p>Serghein: Created page with "This enzymatic technique can be used for cleaving DNA molecules at specific sites, ensuring that all DNA fragments that contain a particular sequence have the same size; furth..."</p>
<hr />
<div>This enzymatic technique can be used for cleaving DNA molecules at specific sites, ensuring that all DNA fragments that contain a particular sequence have the same size; furthermore, each fragment that contains the desired sequence has the sequence located at exactly the same position within the fragment. The cleavage method makes use of an important class of DNA-cleaving enzymes isolated primarily from bacteria. These enzymes are called restriction endonucleases or restriction enzymes, and they are able to cleave DNA molecules at the positions at which particular short sequences of bases are present.<br />
<br />
<h3>References</h3><br />
<ul><br />
<li><i>Hartl, Daniel L., Jones, Elizabeth W. (2001), Genetics: Analysis of Genes and Genomes, Fifth Edition</i></li><br />
</ul></div>
Serghein
https://wiki.tanakalab.org/index.php?title=Overview&diff=303
Overview
2014-03-04T11:09:38Z
<p>Serghein: /* Molecular biology */</p>
<hr />
<div>== Introduction ==<br />
On the pages listed below you can find most common protocols used in the lab as well as a list of lab duties along with the names of the responsible persons. Please, contact the responsible persons if you have any question, suggestions or troubles.<br />
<br />
== Axolotl ==<br />
<br />
=== Maintainance ===<br />
In this section you will find some general information on how to [[Axolotl#Maintaining_the_axolotls|maintain]] the animals.<br />
<br />
=== Feeding ===<br />
This section will give you an overview of how to [[Axolotl#Feeding|feed]] the axolotls.<br />
<br />
=== Interesting observations ===<br />
In the following section you can find some [[Axolotl#Interesting_observations|interesting observations]] concerning the axolotl, its behavior, caveats of the transgenics and many more.<br />
<br />
== Lab duties ==<br />
<ul><br />
=== Chemicals ===<br />
<li>[[Antibiotics|Antibiotics]]</li><br />
<li>[[Benzocaine|Benzocaine]]</li><br />
<li>[[Fibronectin|Fibronectin]]</li><br />
<li>[[Gelatine|Gelatine]]</li><br />
<li>[[Liquid_nitrogen|Liquid nitrogen]]</li><br />
<li>[[Primary_antibodies|Primary antibodies]]</li><br />
<li>[[Secondary_antibodies|Secondary antibodies]]</li><br />
<li>[[Serum_heat_inactivation|Serum heat inactivation]]</li><br />
<br />
=== Hardware ===<br />
<li>[[Autoclave|Autoclave]]</li><br />
<li>[[Cryostat|Cryostat]]</li><br />
<li>[[Dissecting_microscopes|Dissecting microscopes]]</li><br />
<li>[[Leica_confocal_microscope|Leica confocal microscope]]</li><br />
<li>[[Vacuum_pumps|Vacuum pumps]]</li><br />
<li>[[Waterbath|Waterbath]]</li><br />
<br />
=== General ===<br />
<li>[[Ordering_common_stuff|Ordering common stuff]]</li><br />
<li>[[Heat_shock_competent_cells|Heat-shock competent cells]]</li><br />
</ul><br />
<br />
<br />
== Protocols ==<br />
<ul><br />
=== Cell culture ===<br />
<li>[[Blastema_cells|Blastema cells]]</li><br />
<li>[[Baculovirus_titration|Baculovirus titration]]</li><br />
<li>[[Myoblasts_electroporation|Myoblasts electroporation]]</li><br />
<li>[[Adhesive_cell_culture|Adhesive cell culture]]</li><br />
<li>[[Electroporation_of_blastema_cells|Electroporation of blastema cells]]</li><br />
<li>[[Electroporation_of_nec|Electroporation of neural epithelia cells (axolotl spinal cord)]]</li><br />
<li>[[mESC_culture|mESC culture/Cyst formation]]</li><br />
<li>[[Neurosphere_culture|Neurosphere culture]]</li><br />
=== Histology ===<br />
<li>[[Double_Immunostaining_via_antigen_retrieval|Double Immunostaining via antigen retrieval (Sherry)]]</li><br />
=== Molecular biology ===<br />
<ul><br />
<li>[[Metamorphosis_protocol|Metamorphosis protocol (Sherry)]]</li><br />
<li>[[Digestion_DNA|Digestion (Plasmid DNA)]]</li><br />
</ul><br />
<br />
== Lab business ==<br />
=== Ordering database ===<br />
Use the following [http://ordering-db.biotec.tu-dresden.de/ordering/login.gsp ordering database] to place your orders.<br />
<br />
=== Booking calendars ===<br />
Since some pieces of hardware are used intensively it is necessary to book them in advance. The links to the corresponding booking calendars are listed below.<br />
<ul><br />
<li><br />
Fluorescence microscopes<br />
<ul><br />
<li>[http://www.my.calendars.net/olympusszx16 Olympus SZX 16]</li><br />
<li>[http://www.my.calendars.net/new_olympus/ New Olympus SZX 16]</li><br />
<li>[http://www.my.calendars.net/Olympus_OVK Olympus OVK]</li><br />
<li>[http://www.my.calendars.net/axio_observer/ Axio Observer]</li><br />
</ul><br />
</li><br />
<li><br />
Microinjectors and electroporators and dissecting microscope<br />
<ul><br />
<li>Room 0.232<br />
<ul> <br />
<li>[http://www.my.calendars.net/electroporator Nepa Gene]</li><br />
<li>[http://www.my.calendars.net/electroporator2 ECM 830]</li><br />
<li>[http://www.my.calendars.net/stereoscope2/d01/11/2012 Olympus dissecting microscope]</li><br />
</ul><br />
</li><br />
<li>Lab<br />
<ul><br />
<li>[http://www.my.calendars.net/OlympusLab Olympus (next to the axolotls)]</li><br />
<li>[http://www.my.calendars.net/OlympusLab2 Olympus (next to the Microtome)]</li><br />
</ul><br />
</li><br />
</ul><br />
</li><br />
<li><br />
Confocal microscopes<br />
<ul><br />
<li>[http://www.my.calendars.net/leica_lsm Leica LSM]</li><br />
</ul><br />
</li><br />
<li><br />
Cryostats<br />
<ul><br />
<li>[http://www.my.calendars.net/cryostat1 Cryostat 1]</li><br />
<li>[http://www.my.calendars.net/cryostat2 Cryostat 2]</li><br />
</ul><br />
</li><br />
<li><br />
Microtome<br />
<ul><br />
<li>[http://www.my.calendars.net/microtome Microtome]</li><br />
</ul><br />
</li><br />
<li><br />
Paraffin embedding station<br />
<ul><br />
<li>[http://www.my.calendars.net/wax_station Paraffin embedding station]</li><br />
</ul><br />
</li><br />
</ul><br />
<br />
== Genetics ==<br />
=== Transgenic lines ===<br />
<ul><br />
<li>[[Transgenic_axolotl_lines|Axolotl (A.mexicanum)]]</li><br />
<li>[[Transgenic_frog_lines|Frog (X.laevis)]]</li><br />
</ul><br />
<br />
=== Markers ===<br />
{| class="wikitable sortable"<br />
!style="width: 150px" | Marker<br />
!style="width: 250px" | Full name<br />
!style="width: 250px" | Target<br />
!style="width: 450px" | Remarks<br />
!style="width: 200px" | Link<br />
|-<br />
|DAPI/Hoechst<br />
|4',6-diamidino-2-phenylindole<br />
|Nuclei<br />
|Incorporates into the DNA<br />
|[http://en.wikipedia.org/wiki/DAPI DAPI], [http://en.wikipedia.org/wiki/Hoechst_stain Hoechst]<br />
|-<br />
|PCNA<br />
|Proliferating-Cell-Nuclear-Antigen<br />
|Dividing cells<br />
|<br />
|[http://en.wikipedia.org/wiki/PCNA PCNA]<br />
|-<br />
|SOX2<br />
|SRY (sex determining region Y)-box 2<br />
|Preferentially neuronal lineage<br />
|Progenitor marker for both spinal cord and brain<br />
|[http://en.wikipedia.org/wiki/Sox2 SOX2]<br />
|-<br />
|PAX6<br />
|Paired box protein Pax-6<br />
|Brain/spinal cord<br />
|aka aniridia type II protein (AN2) or oculorhombin<br />
|[http://en.wikipedia.org/wiki/Pax6 PAX6]<br />
|-<br />
|PAX7<br />
|Paired box protein Pax-7<br />
|Satellite cells/spinal cord/brain<br />
|<br />
|[http://en.wikipedia.org/wiki/PAX7 PAX7]<br />
|-<br />
|MHC<br />
|Myosin heavy chain<br />
|Muscle fibers<br />
|<br />
|[http://en.wikipedia.org/wiki/Myosin_heavy_chain MHC]<br />
|-<br />
|MYF5<br />
|Myogenic factor 5<br />
|Myoblasts<br />
|Regulates muscle differentiation, labels cycling myoblasts<br />
|[http://en.wikipedia.org/wiki/Myf5 MYF5]<br />
|-<br />
|TUBB3<br />
|ßIII-tubulin<br />
|Axons<br />
|<br />
|[http://en.wikipedia.org/wiki/TUBB3 TUBB3]<br />
|-<br />
|MBP<br />
|Myelin basic protein<br />
|Schwann cells<br />
|<br />
|-<br />
|PRRX1<br />
|Paired mesoderm homeobox protein 1<br />
|Connective tissue progenitors in Limb bud and Limb Blastema<br />
|<br />
|[http://en.wikipedia.org/wiki/PRRX1 PRRX1]<br />
|-<br />
|SMA<br />
|Smooth muscle actin<br />
|Blood vessels/endothelial cells<br />
|<br />
|<br />
|-<br />
|GFAP<br />
|Glial fibrillary acidic protein<br />
|Glia<br />
|<br />
|[http://en.wikipedia.org/wiki/Glial_fibrillary_acidic_protein GFAP]<br />
|-<br />
|NeuN<br />
|Feminizing Locus on X-3, Fox-3, or Hexaribonucleotide Binding Protein-3<br />
|Differentiated nerve<br />
|<br />
|[http://en.wikipedia.org/wiki/NeuN NeuN]<br />
|-<br />
|LEU7/HNK1/B3GAT1/CD57<br />
|Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 1<br />
|Schwann cells<br />
|<br />
|[http://en.wikipedia.org/wiki/B3GAT1 B3GAT1]<br />
|-<br />
|XBRA<br />
|Xbrachyury<br />
|Mesoderm during gastrula stage<br />
|<br />
|[http://en.wikipedia.org/wiki/Brachyury Brachyury]<br />
|-<br />
|MSX1<br />
|Muscle segment homeobox, Msh homeobox 1<br />
|Undifferentiated cells<br />
|Transcriptional repressor during embryogenesis<br />
|[http://en.wikipedia.org/wiki/MSX1 MSX1]<br />
|-<br />
|Trypan blue<br />
|<br />
|Dead tissues or cells<br />
|Vital stain<br />
|[http://en.wikipedia.org/wiki/Trypan_blue Trypan blue]<br />
|-<br />
|MEF2C<br />
|Myocyte-specific enhancer factor 2C<br />
|Differentiated muscle cells<br />
|aka MADS box transcription enhancer factor 2, polypeptide C<br />
|[http://en.wikipedia.org/wiki/Mef2c MEF2C]<br />
|-<br />
|PH3<br />
|Phospho-Histone H3<br />
|Mitotic cells<br />
|<br />
|<br />
|-<br />
|BrdU<br />
|Bromodeoxyuridine<br />
|Cells in S-phase<br />
|<br />
|[http://en.wikipedia.org/wiki/Brdu BrdU]<br />
|-<br />
|CASP3<br />
|Caspase 3<br />
|Dying cells<br />
|<br />
|[http://en.wikipedia.org/wiki/CASP3 CASP3]<br />
|-<br />
|GDF5<br />
|Growth/differentiation factor 5<br />
|Joints<br />
|Joint development marker<br />
|[http://en.wikipedia.org/wiki/GDF5 GDF5]<br />
|-<br />
|Survivin<br />
|<br />
|Cleavage furrow<br />
|aka baculoviral inhibitor of apoptosis repeat-containing 5 or BIRC5<br />
|[http://en.wikipedia.org/wiki/Survivin Survivin]<br />
|-<br />
|MAP2<br />
|Microtubule-associated protein 2<br />
|Neurons<br />
|<br />
|[http://en.wikipedia.org/wiki/MAP2 MAP2]<br />
|-<br />
|SOX9<br />
|SRY (sex determining region Y)-box 2<br />
|Cartillage progenitors<br />
|<br />
|[http://en.wikipedia.org/wiki/Sox9 SOX9]<br />
|-<br />
|MBP<br />
|Myelin basic protein<br />
|Myelin sheath<br />
|<br />
|[http://en.wikipedia.org/wiki/Myelin_basic_protein MBP]<br />
|}<br />
<br />
== Digital data ==<br />
Over the years the members of the lab have produced a lot of different data: Sanger sequences, EST libraries, images and so on. <br />
Select a category from the list below in order to view or download the data.<br />
<br />
=== Fileservers ===<br />
{| class="wikitable"<br />
!style="width: 350px" | Location<br />
!style="width: 250px" | Volume size<br />
!style="width: 350px" | Description<br />
!style="width: 350px" | Access<br />
!style="width: 350px" | Location (console only)<br />
|-<br />
|//biodata/groups/<b>crtd_tanaka</b><br />
|16 TB<br />
|General purpose storage space<br />
|Entire Tanaka lab<br />
|<i>biocluster:</i> <b>/group/crtd_tanaka</b><br />
|-<br />
|//biodata/groups/<b>tanaka-ests</b><br />
|247 GB<br />
|EST sequences<br />
|Entire Tanaka lab<br />
|<i>biocluster:</i> <b>/group/tanaka-ests</b><br />
|-<br />
|//biodata/groups/<b>axolotl-transcriptome</b><br />
|500 GB<br />
|Axolotl transcriptome data<br />
|Elly, Sergej<br />
|<i>biocluster:</i> <b>/projects/axolotl-transcriptome</b><br />
|-<br />
|//biodata/groups/<b>tanaka-saori</b><br />
|878 GB<br />
|Special directory for Saori's data<br />
|Elly, Saori, Sergej<br />
|<i>biocluster:</i> <b>/group/tanaka-saori</b><br />
|}<br />
<br />
{{Tip|The path is different, when accessing the file server from the console.}}<br />
<br />
=== Literature ===<br />
<ul><br />
<li>[[Literature#Theses|Theses]]</li><br />
<li>[[Literature#Publications|Publications]]</li><br />
</ul><br />
<br />
=== Databases ===<br />
<ul><br />
<li>[http://elbrus.biochem.mpg.de/ Axolotl transcriptome] website contains the Axolotl transcriptome assemblies</li><br />
<li>[http://newtomics.mpi-bn.mpg.de/ Newt transcriptome] website contains the Newt transcriptome assembly</li><br />
<li>[http://sandberg.cmb.ki.se/redspottednewt/ Red spotted newt transcriptome] website contains the red spotted newt transcriptome assembly</li><br />
<li>[https://python-srv1.mpi-cbg.de/axolotl/cgi-bin/login.cgi Axolotl EST] database contains several ESTs and also some additional information, e.g. the position of the well with the corresponding insert in the Blastema (BL) or Neural tube (NT) library.</li><br />
<li>[http://python-srv1.mpi-cbg.de/axolotl/cgi-bin/login.cgi?dispatch=contig_search.cgi Short insert cDNA library]</li><br />
<li>CURRENTLY UNAVAILABLE! [http://est.age.mpg.de/ Axologle] database contains expression profiling data of Axolotl limb regeneration</li><br />
<li>CURRENTLY UNAVAILABLE! [http://est.age.mpg.de/blast/blast.html Axolotl BLAST] database contains several different BLAST-able Axolotl transciptome assemblies</li><br />
</ul><br />
<br />
=== Datasets ===<br />
<ul><br />
<li>[[Datasets#Sequences|Sequences]]<br />
<ul><br />
<li>[[Datasets#Illumina|Illumina]]</li><br />
<li>[[Datasets#Sanger|Sanger]]</li><br />
<li>[[Datasets#Roche.2F454|Roche/454]]</li><br />
</ul><br />
</li><br />
<li>[[Datasets#Microarrays|Microarrays]]<br />
</ul><br />
<br />
=== Interesting links ===<br />
<ul><br />
<li>[http://www.nytimes.com/video/2013/02/27/science/100000002087758/finding-the-visible-in-the-invisible.html Visible in the invisible]: a movie introducing a new image processing ana analysis technique developed at the MIT.</li><br />
</ul><br />
<br />
== Lab life ==<br />
<ul><br />
<li>[[Lab_photos|Lab photos]]</li><br />
<li>Further pictures can be found in <b>/biodata/groups/crtd_tanaka/LabFun/</b></li><br />
<li>The recepies for Heino's farewell present can be found under <b>/biodata/groups/crtd_tanaka/LabFun/Heino's farewell present/</b></li><br />
<li>The video of the visit of the EU commissioner can be found under <b>/biodata/groups/crtd_tanaka/LabFun/</b></li><br />
</ul></div>
Serghein
https://wiki.tanakalab.org/index.php?title=Overview&diff=298
Overview
2013-07-24T09:22:42Z
<p>Serghein: </p>
<hr />
<div>== Introduction ==<br />
On the pages listed below you can find most common protocols used in the lab as well as a list of lab duties along with the names of the responsible persons. Please, contact the responsible persons if you have any question, suggestions or troubles.<br />
<br />
== Axolotl ==<br />
<br />
=== Maintainance ===<br />
In this section you will find some general information on how to [[Axolotl#Maintaining_the_axolotls|maintain]] the animals.<br />
<br />
=== Feeding ===<br />
This section will give you an overview of how to [[Axolotl#Feeding|feed]] the axolotls.<br />
<br />
=== Interesting observations ===<br />
In the following section you can find some [[Axolotl#Interesting_observations|interesting observations]] concerning the axolotl, its behavior, caveats of the transgenics and many more.<br />
<br />
== Lab duties ==<br />
<ul><br />
=== Chemicals ===<br />
<li>[[Antibiotics|Antibiotics]]</li><br />
<li>[[Benzocaine|Benzocaine]]</li><br />
<li>[[Fibronectin|Fibronectin]]</li><br />
<li>[[Gelatine|Gelatine]]</li><br />
<li>[[Liquid_nitrogen|Liquid nitrogen]]</li><br />
<li>[[Primary_antibodies|Primary antibodies]]</li><br />
<li>[[Secondary_antibodies|Secondary antibodies]]</li><br />
<li>[[Serum_heat_inactivation|Serum heat inactivation]]</li><br />
<br />
=== Hardware ===<br />
<li>[[Autoclave|Autoclave]]</li><br />
<li>[[Cryostat|Cryostat]]</li><br />
<li>[[Dissecting_microscopes|Dissecting microscopes]]</li><br />
<li>[[Leica_confocal_microscope|Leica confocal microscope]]</li><br />
<li>[[Vacuum_pumps|Vacuum pumps]]</li><br />
<li>[[Waterbath|Waterbath]]</li><br />
<br />
=== General ===<br />
<li>[[Ordering_common_stuff|Ordering common stuff]]</li><br />
<li>[[Heat_shock_competent_cells|Heat-shock competent cells]]</li><br />
</ul><br />
<br />
<br />
== Protocols ==<br />
<ul><br />
=== Cell culture ===<br />
<li>[[Blastema_cells|Blastema cells]]</li><br />
<li>[[Baculovirus_titration|Baculovirus titration]]</li><br />
<li>[[Myoblasts_electroporation|Myoblasts electroporation]]</li><br />
<li>[[Adhesive_cell_culture|Adhesive cell culture]]</li><br />
<li>[[Electroporation_of_blastema_cells|Electroporation of blastema cells]]</li><br />
<li>[[Electroporation_of_nec|Electroporation of neural epithelia cells (axolotl spinal cord)]]</li><br />
<li>[[mESC_culture|mESC culture/Cyst formation]]</li><br />
<li>[[Neurosphere_culture|Neurosphere culture]]</li><br />
=== Histology ===<br />
<li>[[Double_Immunostaining_via_antigen_retrieval|Double Immunostaining via antigen retrieval (Sherry)]]</li><br />
=== Molecular biology ===<br />
<li>[[Metamorphosis_protocol|Metamorphosis protocol (Sherry)]]</li><br />
</ul><br />
<br />
== Lab business ==<br />
=== Ordering database ===<br />
Use the following [http://ordering-db.biotec.tu-dresden.de/ordering/login.gsp ordering database] to place your orders.<br />
<br />
=== Booking calendars ===<br />
Since some pieces of hardware are used intensively it is necessary to book them in advance. The links to the corresponding booking calendars are listed below.<br />
<ul><br />
<li><br />
Fluorescence microscopes<br />
<ul><br />
<li>[http://www.my.calendars.net/olympusszx16 Olympus SZX 16]</li><br />
<li>[http://www.my.calendars.net/new_olympus/ New Olympus SZX 16]</li><br />
<li>[http://www.my.calendars.net/Olympus_OVK Olympus OVK]</li><br />
<li>[http://www.my.calendars.net/axio_observer/ Axio Observer]</li><br />
</ul><br />
</li><br />
<li><br />
Microinjectors and electroporators and dissecting microscope<br />
<ul><br />
<li>Room 0.232<br />
<ul> <br />
<li>[http://www.my.calendars.net/electroporator Nepa Gene]</li><br />
<li>[http://www.my.calendars.net/electroporator2 ECM 830]</li><br />
<li>[http://www.my.calendars.net/stereoscope2/d01/11/2012 Olympus dissecting microscope]</li><br />
</ul><br />
</li><br />
<li>Lab<br />
<ul><br />
<li>[http://www.my.calendars.net/OlympusLab Olympus (next to the axolotls)]</li><br />
<li>[http://www.my.calendars.net/OlympusLab2 Olympus (next to the Microtome)]</li><br />
</ul><br />
</li><br />
</ul><br />
</li><br />
<li><br />
Confocal microscopes<br />
<ul><br />
<li>[http://www.my.calendars.net/leica_lsm Leica LSM]</li><br />
</ul><br />
</li><br />
<li><br />
Cryostats<br />
<ul><br />
<li>[http://www.my.calendars.net/cryostat1 Cryostat 1]</li><br />
<li>[http://www.my.calendars.net/cryostat2 Cryostat 2]</li><br />
</ul><br />
</li><br />
<li><br />
Microtome<br />
<ul><br />
<li>[http://www.my.calendars.net/microtome Microtome]</li><br />
</ul><br />
</li><br />
<li><br />
Paraffin embedding station<br />
<ul><br />
<li>[http://www.my.calendars.net/wax_station Paraffin embedding station]</li><br />
</ul><br />
</li><br />
</ul><br />
<br />
== Genetics ==<br />
=== Transgenic lines ===<br />
<ul><br />
<li>[[Transgenic_axolotl_lines|Axolotl (A.mexicanum)]]</li><br />
<li>[[Transgenic_frog_lines|Frog (X.laevis)]]</li><br />
</ul><br />
<br />
=== Markers ===<br />
{| class="wikitable sortable"<br />
!style="width: 150px" | Marker<br />
!style="width: 250px" | Full name<br />
!style="width: 250px" | Target<br />
!style="width: 450px" | Remarks<br />
!style="width: 200px" | Link<br />
|-<br />
|DAPI/Hoechst<br />
|4',6-diamidino-2-phenylindole<br />
|Nuclei<br />
|Incorporates into the DNA<br />
|[http://en.wikipedia.org/wiki/DAPI DAPI], [http://en.wikipedia.org/wiki/Hoechst_stain Hoechst]<br />
|-<br />
|PCNA<br />
|Proliferating-Cell-Nuclear-Antigen<br />
|Dividing cells<br />
|<br />
|[http://en.wikipedia.org/wiki/PCNA PCNA]<br />
|-<br />
|SOX2<br />
|SRY (sex determining region Y)-box 2<br />
|Preferentially neuronal lineage<br />
|Progenitor marker for both spinal cord and brain<br />
|[http://en.wikipedia.org/wiki/Sox2 SOX2]<br />
|-<br />
|PAX6<br />
|Paired box protein Pax-6<br />
|Brain/spinal cord<br />
|aka aniridia type II protein (AN2) or oculorhombin<br />
|[http://en.wikipedia.org/wiki/Pax6 PAX6]<br />
|-<br />
|PAX7<br />
|Paired box protein Pax-7<br />
|Satellite cells/spinal cord/brain<br />
|<br />
|[http://en.wikipedia.org/wiki/PAX7 PAX7]<br />
|-<br />
|MHC<br />
|Myosin heavy chain<br />
|Muscle fibers<br />
|<br />
|[http://en.wikipedia.org/wiki/Myosin_heavy_chain MHC]<br />
|-<br />
|MYF5<br />
|Myogenic factor 5<br />
|Myoblasts<br />
|Regulates muscle differentiation, labels cycling myoblasts<br />
|[http://en.wikipedia.org/wiki/Myf5 MYF5]<br />
|-<br />
|TUBB3<br />
|ßIII-tubulin<br />
|Axons<br />
|<br />
|[http://en.wikipedia.org/wiki/TUBB3 TUBB3]<br />
|-<br />
|MBP<br />
|Myelin basic protein<br />
|Schwann cells<br />
|<br />
|-<br />
|PRRX1<br />
|Paired mesoderm homeobox protein 1<br />
|Connective tissue progenitors in Limb bud and Limb Blastema<br />
|<br />
|[http://en.wikipedia.org/wiki/PRRX1 PRRX1]<br />
|-<br />
|SMA<br />
|Smooth muscle actin<br />
|Blood vessels/endothelial cells<br />
|<br />
|<br />
|-<br />
|GFAP<br />
|Glial fibrillary acidic protein<br />
|Glia<br />
|<br />
|[http://en.wikipedia.org/wiki/Glial_fibrillary_acidic_protein GFAP]<br />
|-<br />
|NeuN<br />
|Feminizing Locus on X-3, Fox-3, or Hexaribonucleotide Binding Protein-3<br />
|Differentiated nerve<br />
|<br />
|[http://en.wikipedia.org/wiki/NeuN NeuN]<br />
|-<br />
|LEU7/HNK1/B3GAT1/CD57<br />
|Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 1<br />
|Schwann cells<br />
|<br />
|[http://en.wikipedia.org/wiki/B3GAT1 B3GAT1]<br />
|-<br />
|XBRA<br />
|Xbrachyury<br />
|Mesoderm during gastrula stage<br />
|<br />
|[http://en.wikipedia.org/wiki/Brachyury Brachyury]<br />
|-<br />
|MSX1<br />
|Muscle segment homeobox, Msh homeobox 1<br />
|Undifferentiated cells<br />
|Transcriptional repressor during embryogenesis<br />
|[http://en.wikipedia.org/wiki/MSX1 MSX1]<br />
|-<br />
|Trypan blue<br />
|<br />
|Dead tissues or cells<br />
|Vital stain<br />
|[http://en.wikipedia.org/wiki/Trypan_blue Trypan blue]<br />
|-<br />
|MEF2C<br />
|Myocyte-specific enhancer factor 2C<br />
|Differentiated muscle cells<br />
|aka MADS box transcription enhancer factor 2, polypeptide C<br />
|[http://en.wikipedia.org/wiki/Mef2c MEF2C]<br />
|-<br />
|PH3<br />
|Phospho-Histone H3<br />
|Mitotic cells<br />
|<br />
|<br />
|-<br />
|BrdU<br />
|Bromodeoxyuridine<br />
|Cells in S-phase<br />
|<br />
|[http://en.wikipedia.org/wiki/Brdu BrdU]<br />
|-<br />
|CASP3<br />
|Caspase 3<br />
|Dying cells<br />
|<br />
|[http://en.wikipedia.org/wiki/CASP3 CASP3]<br />
|-<br />
|GDF5<br />
|Growth/differentiation factor 5<br />
|Joints<br />
|Joint development marker<br />
|[http://en.wikipedia.org/wiki/GDF5 GDF5]<br />
|-<br />
|Survivin<br />
|<br />
|Cleavage furrow<br />
|aka baculoviral inhibitor of apoptosis repeat-containing 5 or BIRC5<br />
|[http://en.wikipedia.org/wiki/Survivin Survivin]<br />
|-<br />
|MAP2<br />
|Microtubule-associated protein 2<br />
|Neurons<br />
|<br />
|[http://en.wikipedia.org/wiki/MAP2 MAP2]<br />
|-<br />
|SOX9<br />
|SRY (sex determining region Y)-box 2<br />
|Cartillage progenitors<br />
|<br />
|[http://en.wikipedia.org/wiki/Sox9 SOX9]<br />
|-<br />
|MBP<br />
|Myelin basic protein<br />
|Myelin sheath<br />
|<br />
|[http://en.wikipedia.org/wiki/Myelin_basic_protein MBP]<br />
|}<br />
<br />
== Digital data ==<br />
Over the years the members of the lab have produced a lot of different data: Sanger sequences, EST libraries, images and so on. <br />
Select a category from the list below in order to view or download the data.<br />
<br />
=== Fileservers ===<br />
{| class="wikitable"<br />
!style="width: 350px" | Location<br />
!style="width: 250px" | Volume size<br />
!style="width: 350px" | Description<br />
!style="width: 350px" | Access<br />
!style="width: 350px" | Location (console only)<br />
|-<br />
|//biodata/groups/<b>crtd_tanaka</b><br />
|16 TB<br />
|General purpose storage space<br />
|Entire Tanaka lab<br />
|<i>biocluster:</i> <b>/group/crtd_tanaka</b><br />
|-<br />
|//biodata/groups/<b>tanaka-ests</b><br />
|247 GB<br />
|EST sequences<br />
|Entire Tanaka lab<br />
|<i>biocluster:</i> <b>/group/tanaka-ests</b><br />
|-<br />
|//biodata/groups/<b>axolotl-transcriptome</b><br />
|500 GB<br />
|Axolotl transcriptome data<br />
|Elly, Sergej<br />
|<i>biocluster:</i> <b>/projects/axolotl-transcriptome</b><br />
|-<br />
|//biodata/groups/<b>tanaka-saori</b><br />
|878 GB<br />
|Special directory for Saori's data<br />
|Elly, Saori, Sergej<br />
|<i>biocluster:</i> <b>/group/tanaka-saori</b><br />
|}<br />
<br />
{{Tip|The path is different, when accessing the file server from the console.}}<br />
<br />
=== Literature ===<br />
<ul><br />
<li>[[Literature#Theses|Theses]]</li><br />
<li>[[Literature#Publications|Publications]]</li><br />
</ul><br />
<br />
=== Databases ===<br />
<ul><br />
<li>[http://elbrus.biochem.mpg.de/ Axolotl transcriptome] website contains the Axolotl transcriptome assemblies</li><br />
<li>[http://newtomics.mpi-bn.mpg.de/ Newt transcriptome] website contains the Newt transcriptome assembly</li><br />
<li>[http://sandberg.cmb.ki.se/redspottednewt/ Red spotted newt transcriptome] website contains the red spotted newt transcriptome assembly</li><br />
<li>[https://python-srv1.mpi-cbg.de/axolotl/cgi-bin/login.cgi Axolotl EST] database contains several ESTs and also some additional information, e.g. the position of the well with the corresponding insert in the Blastema (BL) or Neural tube (NT) library.</li><br />
<li>CURRENTLY UNAVAILABLE! [http://est.age.mpg.de/ Axologle] database contains expression profiling data of Axolotl limb regeneration</li><br />
<li>CURRENTLY UNAVAILABLE! [http://est.age.mpg.de/blast/blast.html Axolotl BLAST] database contains several different BLAST-able Axolotl transciptome assemblies</li><br />
</ul><br />
<br />
=== Datasets ===<br />
<ul><br />
<li>[[Datasets#Sequences|Sequences]]<br />
<ul><br />
<li>[[Datasets#Illumina|Illumina]]</li><br />
<li>[[Datasets#Sanger|Sanger]]</li><br />
<li>[[Datasets#Roche.2F454|Roche/454]]</li><br />
</ul><br />
</li><br />
<li>[[Datasets#Microarrays|Microarrays]]<br />
</ul><br />
<br />
=== Interesting links ===<br />
<ul><br />
<li>[http://www.nytimes.com/video/2013/02/27/science/100000002087758/finding-the-visible-in-the-invisible.html Visible in the invisible]: a movie introducing a new image processing ana analysis technique developed at the MIT.</li><br />
</ul><br />
<br />
== Lab life ==<br />
<ul><br />
<li>[[Lab_photos|Lab photos]]</li><br />
<li>Further pictures can be found in <b>/biodata/groups/crtd_tanaka/LabFun/</b></li><br />
<li>The recepies for Heino's farewell present can be found under <b>/biodata/groups/crtd_tanaka/LabFun/Heino's farewell present/</b></li><br />
<li>The video of the visit of the EU commissioner can be found under <b>/biodata/groups/crtd_tanaka/LabFun/</b></li><br />
</ul></div>
Serghein
https://wiki.tanakalab.org/index.php?title=Overview&diff=297
Overview
2013-07-24T09:21:14Z
<p>Serghein: /* Databases */</p>
<hr />
<div>== Introduction ==<br />
On the pages listed below you can find most common protocols used in the lab as well as a list of lab duties along with the names of the responsible persons. Please, contact the responsible persons if you have any question, suggestions or troubles.<br />
<br />
== Axolotl ==<br />
<br />
=== Maintainance ===<br />
In this section you will find some general information on how to [[Axolotl#Maintaining_the_axolotls|maintain]] the animals.<br />
<br />
=== Feeding ===<br />
This section will give you an overview of how to [[Axolotl#Feeding|feed]] the axolotls.<br />
<br />
=== Interesting observations ===<br />
In the following section you can find some [[Axolotl#Interesting_observations|interesting observations]] concerning the axolotl, its behavior, caveats of the transgenics and many more.<br />
<br />
== Lab duties ==<br />
<ul><br />
=== Chemicals ===<br />
<li>[[Antibiotics|Antibiotics]]</li><br />
<li>[[Benzocaine|Benzocaine]]</li><br />
<li>[[Fibronectin|Fibronectin]]</li><br />
<li>[[Gelatine|Gelatine]]</li><br />
<li>[[Liquid_nitrogen|Liquid nitrogen]]</li><br />
<li>[[Primary_antibodies|Primary antibodies]]</li><br />
<li>[[Secondary_antibodies|Secondary antibodies]]</li><br />
<li>[[Serum_heat_inactivation|Serum heat inactivation]]</li><br />
<br />
=== Hardware ===<br />
<li>[[Autoclave|Autoclave]]</li><br />
<li>[[Cryostat|Cryostat]]</li><br />
<li>[[Dissecting_microscopes|Dissecting microscopes]]</li><br />
<li>[[Leica_confocal_microscope|Leica confocal microscope]]</li><br />
<li>[[Vacuum_pumps|Vacuum pumps]]</li><br />
<li>[[Waterbath|Waterbath]]</li><br />
<br />
=== General ===<br />
<li>[[Ordering_common_stuff|Ordering common stuff]]</li><br />
<li>[[Heat_shock_competent_cells|Heat-shock competent cells]]</li><br />
</ul><br />
<br />
<br />
== Protocols ==<br />
<ul><br />
=== Cell culture ===<br />
<li>[[Blastema_cells|Blastema cells]]</li><br />
<li>[[Baculovirus_titration|Baculovirus titration]]</li><br />
<li>[[Myoblasts_electroporation|Myoblasts electroporation]]</li><br />
<li>[[Adhesive_cell_culture|Adhesive cell culture]]</li><br />
<li>[[Electroporation_of_blastema_cells|Electroporation of blastema cells]]</li><br />
<li>[[Electroporation_of_nec|Electroporation of neural epithelia cells (axolotl spinal cord)]]</li><br />
<li>[[mESC_culture|mESC culture/Cyst formation]]</li><br />
<li>[[Neurosphere_culture|Neurosphere culture]]</li><br />
=== Histology ===<br />
<li>[[Double_Immunostaining_via_antigen_retrieval|Double Immunostaining via antigen retrieval (Sherry)]]</li><br />
=== Molecular biology ===<br />
<li>[[Metamorphosis_protocol|Metamorphosis protocol (Sherry)]]</li><br />
</ul><br />
<br />
== Booking calendars ==<br />
Since some pieces of hardware are used intensively it is necessary to book them in advance. The links to the corresponding booking calendars are listed below.<br />
<ul><br />
<li><br />
Fluorescence microscopes<br />
<ul><br />
<li>[http://www.my.calendars.net/olympusszx16 Olympus SZX 16]</li><br />
<li>[http://www.my.calendars.net/new_olympus/ New Olympus SZX 16]</li><br />
<li>[http://www.my.calendars.net/Olympus_OVK Olympus OVK]</li><br />
<li>[http://www.my.calendars.net/axio_observer/ Axio Observer]</li><br />
</ul><br />
</li><br />
<li><br />
Microinjectors and electroporators and dissecting microscope<br />
<ul><br />
<li>Room 0.232<br />
<ul> <br />
<li>[http://www.my.calendars.net/electroporator Nepa Gene]</li><br />
<li>[http://www.my.calendars.net/electroporator2 ECM 830]</li><br />
<li>[http://www.my.calendars.net/stereoscope2/d01/11/2012 Olympus dissecting microscope]</li><br />
</ul><br />
</li><br />
<li>Lab<br />
<ul><br />
<li>[http://www.my.calendars.net/OlympusLab Olympus (next to the axolotls)]</li><br />
<li>[http://www.my.calendars.net/OlympusLab2 Olympus (next to the Microtome)]</li><br />
</ul><br />
</li><br />
</ul><br />
</li><br />
<li><br />
Confocal microscopes<br />
<ul><br />
<li>[http://www.my.calendars.net/leica_lsm Leica LSM]</li><br />
</ul><br />
</li><br />
<li><br />
Cryostats<br />
<ul><br />
<li>[http://www.my.calendars.net/cryostat1 Cryostat 1]</li><br />
<li>[http://www.my.calendars.net/cryostat2 Cryostat 2]</li><br />
</ul><br />
</li><br />
<li><br />
Microtome<br />
<ul><br />
<li>[http://www.my.calendars.net/microtome Microtome]</li><br />
</ul><br />
</li><br />
<li><br />
Paraffin embedding station<br />
<ul><br />
<li>[http://www.my.calendars.net/wax_station Paraffin embedding station]</li><br />
</ul><br />
</li><br />
</ul><br />
<br />
== Genetics ==<br />
=== Transgenic lines ===<br />
<ul><br />
<li>[[Transgenic_axolotl_lines|Axolotl (A.mexicanum)]]</li><br />
<li>[[Transgenic_frog_lines|Frog (X.laevis)]]</li><br />
</ul><br />
<br />
=== Markers ===<br />
{| class="wikitable sortable"<br />
!style="width: 150px" | Marker<br />
!style="width: 250px" | Full name<br />
!style="width: 250px" | Target<br />
!style="width: 450px" | Remarks<br />
!style="width: 200px" | Link<br />
|-<br />
|DAPI/Hoechst<br />
|4',6-diamidino-2-phenylindole<br />
|Nuclei<br />
|Incorporates into the DNA<br />
|[http://en.wikipedia.org/wiki/DAPI DAPI], [http://en.wikipedia.org/wiki/Hoechst_stain Hoechst]<br />
|-<br />
|PCNA<br />
|Proliferating-Cell-Nuclear-Antigen<br />
|Dividing cells<br />
|<br />
|[http://en.wikipedia.org/wiki/PCNA PCNA]<br />
|-<br />
|SOX2<br />
|SRY (sex determining region Y)-box 2<br />
|Preferentially neuronal lineage<br />
|Progenitor marker for both spinal cord and brain<br />
|[http://en.wikipedia.org/wiki/Sox2 SOX2]<br />
|-<br />
|PAX6<br />
|Paired box protein Pax-6<br />
|Brain/spinal cord<br />
|aka aniridia type II protein (AN2) or oculorhombin<br />
|[http://en.wikipedia.org/wiki/Pax6 PAX6]<br />
|-<br />
|PAX7<br />
|Paired box protein Pax-7<br />
|Satellite cells/spinal cord/brain<br />
|<br />
|[http://en.wikipedia.org/wiki/PAX7 PAX7]<br />
|-<br />
|MHC<br />
|Myosin heavy chain<br />
|Muscle fibers<br />
|<br />
|[http://en.wikipedia.org/wiki/Myosin_heavy_chain MHC]<br />
|-<br />
|MYF5<br />
|Myogenic factor 5<br />
|Myoblasts<br />
|Regulates muscle differentiation, labels cycling myoblasts<br />
|[http://en.wikipedia.org/wiki/Myf5 MYF5]<br />
|-<br />
|TUBB3<br />
|ßIII-tubulin<br />
|Axons<br />
|<br />
|[http://en.wikipedia.org/wiki/TUBB3 TUBB3]<br />
|-<br />
|MBP<br />
|Myelin basic protein<br />
|Schwann cells<br />
|<br />
|-<br />
|PRRX1<br />
|Paired mesoderm homeobox protein 1<br />
|Connective tissue progenitors in Limb bud and Limb Blastema<br />
|<br />
|[http://en.wikipedia.org/wiki/PRRX1 PRRX1]<br />
|-<br />
|SMA<br />
|Smooth muscle actin<br />
|Blood vessels/endothelial cells<br />
|<br />
|<br />
|-<br />
|GFAP<br />
|Glial fibrillary acidic protein<br />
|Glia<br />
|<br />
|[http://en.wikipedia.org/wiki/Glial_fibrillary_acidic_protein GFAP]<br />
|-<br />
|NeuN<br />
|Feminizing Locus on X-3, Fox-3, or Hexaribonucleotide Binding Protein-3<br />
|Differentiated nerve<br />
|<br />
|[http://en.wikipedia.org/wiki/NeuN NeuN]<br />
|-<br />
|LEU7/HNK1/B3GAT1/CD57<br />
|Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 1<br />
|Schwann cells<br />
|<br />
|[http://en.wikipedia.org/wiki/B3GAT1 B3GAT1]<br />
|-<br />
|XBRA<br />
|Xbrachyury<br />
|Mesoderm during gastrula stage<br />
|<br />
|[http://en.wikipedia.org/wiki/Brachyury Brachyury]<br />
|-<br />
|MSX1<br />
|Muscle segment homeobox, Msh homeobox 1<br />
|Undifferentiated cells<br />
|Transcriptional repressor during embryogenesis<br />
|[http://en.wikipedia.org/wiki/MSX1 MSX1]<br />
|-<br />
|Trypan blue<br />
|<br />
|Dead tissues or cells<br />
|Vital stain<br />
|[http://en.wikipedia.org/wiki/Trypan_blue Trypan blue]<br />
|-<br />
|MEF2C<br />
|Myocyte-specific enhancer factor 2C<br />
|Differentiated muscle cells<br />
|aka MADS box transcription enhancer factor 2, polypeptide C<br />
|[http://en.wikipedia.org/wiki/Mef2c MEF2C]<br />
|-<br />
|PH3<br />
|Phospho-Histone H3<br />
|Mitotic cells<br />
|<br />
|<br />
|-<br />
|BrdU<br />
|Bromodeoxyuridine<br />
|Cells in S-phase<br />
|<br />
|[http://en.wikipedia.org/wiki/Brdu BrdU]<br />
|-<br />
|CASP3<br />
|Caspase 3<br />
|Dying cells<br />
|<br />
|[http://en.wikipedia.org/wiki/CASP3 CASP3]<br />
|-<br />
|GDF5<br />
|Growth/differentiation factor 5<br />
|Joints<br />
|Joint development marker<br />
|[http://en.wikipedia.org/wiki/GDF5 GDF5]<br />
|-<br />
|Survivin<br />
|<br />
|Cleavage furrow<br />
|aka baculoviral inhibitor of apoptosis repeat-containing 5 or BIRC5<br />
|[http://en.wikipedia.org/wiki/Survivin Survivin]<br />
|-<br />
|MAP2<br />
|Microtubule-associated protein 2<br />
|Neurons<br />
|<br />
|[http://en.wikipedia.org/wiki/MAP2 MAP2]<br />
|-<br />
|SOX9<br />
|SRY (sex determining region Y)-box 2<br />
|Cartillage progenitors<br />
|<br />
|[http://en.wikipedia.org/wiki/Sox9 SOX9]<br />
|-<br />
|MBP<br />
|Myelin basic protein<br />
|Myelin sheath<br />
|<br />
|[http://en.wikipedia.org/wiki/Myelin_basic_protein MBP]<br />
|}<br />
<br />
== Digital data ==<br />
Over the years the members of the lab have produced a lot of different data: Sanger sequences, EST libraries, images and so on. <br />
Select a category from the list below in order to view or download the data.<br />
<br />
=== Fileservers ===<br />
{| class="wikitable"<br />
!style="width: 350px" | Location<br />
!style="width: 250px" | Volume size<br />
!style="width: 350px" | Description<br />
!style="width: 350px" | Access<br />
!style="width: 350px" | Location (console only)<br />
|-<br />
|//biodata/groups/<b>crtd_tanaka</b><br />
|16 TB<br />
|General purpose storage space<br />
|Entire Tanaka lab<br />
|<i>biocluster:</i> <b>/group/crtd_tanaka</b><br />
|-<br />
|//biodata/groups/<b>tanaka-ests</b><br />
|247 GB<br />
|EST sequences<br />
|Entire Tanaka lab<br />
|<i>biocluster:</i> <b>/group/tanaka-ests</b><br />
|-<br />
|//biodata/groups/<b>axolotl-transcriptome</b><br />
|500 GB<br />
|Axolotl transcriptome data<br />
|Elly, Sergej<br />
|<i>biocluster:</i> <b>/projects/axolotl-transcriptome</b><br />
|-<br />
|//biodata/groups/<b>tanaka-saori</b><br />
|878 GB<br />
|Special directory for Saori's data<br />
|Elly, Saori, Sergej<br />
|<i>biocluster:</i> <b>/group/tanaka-saori</b><br />
|}<br />
<br />
{{Tip|The path is different, when accessing the file server from the console.}}<br />
<br />
=== Literature ===<br />
<ul><br />
<li>[[Literature#Theses|Theses]]</li><br />
<li>[[Literature#Publications|Publications]]</li><br />
</ul><br />
<br />
=== Databases ===<br />
<ul><br />
<li>[http://elbrus.biochem.mpg.de/ Axolotl transcriptome] website contains the Axolotl transcriptome assemblies</li><br />
<li>[http://newtomics.mpi-bn.mpg.de/ Newt transcriptome] website contains the Newt transcriptome assembly</li><br />
<li>[http://sandberg.cmb.ki.se/redspottednewt/ Red spotted newt transcriptome] website contains the red spotted newt transcriptome assembly</li><br />
<li>[https://python-srv1.mpi-cbg.de/axolotl/cgi-bin/login.cgi Axolotl EST] database contains several ESTs and also some additional information, e.g. the position of the well with the corresponding insert in the Blastema (BL) or Neural tube (NT) library.</li><br />
<li>CURRENTLY UNAVAILABLE! [http://est.age.mpg.de/ Axologle] database contains expression profiling data of Axolotl limb regeneration</li><br />
<li>CURRENTLY UNAVAILABLE! [http://est.age.mpg.de/blast/blast.html Axolotl BLAST] database contains several different BLAST-able Axolotl transciptome assemblies</li><br />
</ul><br />
<br />
=== Datasets ===<br />
<ul><br />
<li>[[Datasets#Sequences|Sequences]]<br />
<ul><br />
<li>[[Datasets#Illumina|Illumina]]</li><br />
<li>[[Datasets#Sanger|Sanger]]</li><br />
<li>[[Datasets#Roche.2F454|Roche/454]]</li><br />
</ul><br />
</li><br />
<li>[[Datasets#Microarrays|Microarrays]]<br />
</ul><br />
<br />
=== Interesting links ===<br />
<ul><br />
<li>[http://www.nytimes.com/video/2013/02/27/science/100000002087758/finding-the-visible-in-the-invisible.html Visible in the invisible]: a movie introducing a new image processing ana analysis technique developed at the MIT.</li><br />
</ul><br />
<br />
== Lab life ==<br />
<ul><br />
<li>[[Lab_photos|Lab photos]]</li><br />
<li>Further pictures can be found in <b>/biodata/groups/crtd_tanaka/LabFun/</b></li><br />
<li>The recepies for Heino's farewell present can be found under <b>/biodata/groups/crtd_tanaka/LabFun/Heino's farewell present/</b></li><br />
<li>The video of the visit of the EU commissioner can be found under <b>/biodata/groups/crtd_tanaka/LabFun/</b></li><br />
</ul></div>
Serghein
https://wiki.tanakalab.org/index.php?title=Overview&diff=289
Overview
2013-07-16T14:19:33Z
<p>Serghein: /* Markers */</p>
<hr />
<div>== Introduction ==<br />
On the pages listed below you can find most common protocols used in the lab as well as a list of lab duties along with the names of the responsible persons. Please, contact the responsible persons if you have any question, suggestions or troubles.<br />
<br />
== Axolotl ==<br />
<br />
=== Maintainance ===<br />
In this section you will find some general information on how to [[Axolotl#Maintaining_the_axolotls|maintain]] the animals.<br />
<br />
=== Feeding ===<br />
This section will give you an overview of how to [[Axolotl#Feeding|feed]] the axolotls.<br />
<br />
=== Interesting observations ===<br />
In the following section you can find some [[Axolotl#Interesting_observations|interesting observations]] concerning the axolotl, its behavior, caveats of the transgenics and many more.<br />
<br />
== Lab duties ==<br />
<ul><br />
=== Chemicals ===<br />
<li>[[Antibiotics|Antibiotics]]</li><br />
<li>[[Benzocaine|Benzocaine]]</li><br />
<li>[[Fibronectin|Fibronectin]]</li><br />
<li>[[Gelatine|Gelatine]]</li><br />
<li>[[Liquid_nitrogen|Liquid nitrogen]]</li><br />
<li>[[Primary_antibodies|Primary antibodies]]</li><br />
<li>[[Secondary_antibodies|Secondary antibodies]]</li><br />
<li>[[Serum_immunostaining|Serum immunostaining]]</li><br />
<br />
=== Hardware ===<br />
<li>[[Autoclave|Autoclave]]</li><br />
<li>[[Cryostat|Cryostat]]</li><br />
<li>[[Dissecting_microscopes|Dissecting microscopes]]</li><br />
<li>[[Leica_confocal_microscope|Leica confocal microscope]]</li><br />
<li>[[Vacuum_pumps|Vacuum pumps]]</li><br />
<li>[[Waterbath|Waterbath]]</li><br />
<br />
=== General ===<br />
<li>[[Ordering_common_stuff|Ordering common stuff]]</li><br />
<li>[[Heat_shock_competent_cells|Heat-shock competent cells]]</li><br />
</ul><br />
<br />
<br />
== Protocols ==<br />
<ul><br />
=== Cell culture ===<br />
<li>[[Blastema_cells|Blastema cells]]</li><br />
<li>[[Baculovirus_titration|Baculovirus titration]]</li><br />
<li>[[Myoblasts_electroporation|Myoblasts electroporation]]</li><br />
<li>[[Adhesive_cell_culture|Adhesive cell culture]]</li><br />
<li>[[Electroporation_of_blastema_cells|Electroporation of blastema cells]]</li><br />
<li>[[Electroporation_of_nec|Electroporation of neural epithelia cells (axolotl spinal cord)]]</li><br />
<li>[[mESC_culture|mESC culture/Cyst formation]]</li><br />
<li>[[Neurosphere_culture|Neurosphere culture]]</li><br />
=== Histology ===<br />
<li>[[Double_Immunostaining_via_antigen_retrieval|Double Immunostaining via antigen retrieval (Sherry)]]</li><br />
=== Molecular biology ===<br />
<li>[[Metamorphosis_protocol|Metamorphosis protocol (Sherry)]]</li><br />
</ul><br />
<br />
== Booking calendars ==<br />
Since some pieces of hardware are used intensively it is necessary to book them in advance. The links to the corresponding booking calendars are listed below.<br />
<ul><br />
<li><br />
Fluorescence microscopes<br />
<ul><br />
<li>[http://www.my.calendars.net/olympusszx16 Olympus SZX 16]</li><br />
<li>[http://www.my.calendars.net/new_olympus/ New Olympus SZX 16]</li><br />
<li>[http://www.my.calendars.net/Olympus_OVK Olympus OVK]</li><br />
<li>[http://www.my.calendars.net/axio_observer/ Axio Observer]</li><br />
</ul><br />
</li><br />
<li><br />
Microinjectors and electroporators and dissecting microscope<br />
<ul><br />
<li>Room 0.232<br />
<ul> <br />
<li>[http://www.my.calendars.net/electroporator Nepa Gene]</li><br />
<li>[http://www.my.calendars.net/electroporator2 ECM 830]</li><br />
<li>[http://www.my.calendars.net/stereoscope2/d01/11/2012 Olympus dissecting microscope]</li><br />
</ul><br />
</li><br />
<li>Lab<br />
<ul><br />
<li>[http://www.my.calendars.net/OlympusLab Olympus (next to the axolotls)]</li><br />
<li>[http://www.my.calendars.net/OlympusLab2 Olympus (next to the Microtome)]</li><br />
</ul><br />
</li><br />
</ul><br />
</li><br />
<li><br />
Confocal microscopes<br />
<ul><br />
<li>[http://www.my.calendars.net/leica_lsm Leica LSM]</li><br />
</ul><br />
</li><br />
<li><br />
Cryostats<br />
<ul><br />
<li>[http://www.my.calendars.net/cryostat1 Cryostat 1]</li><br />
<li>[http://www.my.calendars.net/cryostat2 Cryostat 2]</li><br />
</ul><br />
</li><br />
<li><br />
Microtome<br />
<ul><br />
<li>[http://www.my.calendars.net/microtome Microtome]</li><br />
</ul><br />
</li><br />
<li><br />
Paraffin embedding station<br />
<ul><br />
<li>[http://www.my.calendars.net/wax_station Paraffin embedding station]</li><br />
</ul><br />
</li><br />
</ul><br />
<br />
== Genetics ==<br />
=== Transgenic lines ===<br />
<ul><br />
<li>[[Transgenic_axolotl_lines|Axolotl (A.mexicanum)]]</li><br />
<li>[[Transgenic_frog_lines|Frog (X.laevis)]]</li><br />
</ul><br />
<br />
=== Markers ===<br />
{| class="wikitable sortable"<br />
!style="width: 150px" | Marker<br />
!style="width: 250px" | Full name<br />
!style="width: 250px" | Target<br />
!style="width: 450px" | Remarks<br />
!style="width: 200px" | Link<br />
|-<br />
|DAPI/Hoechst<br />
|4',6-diamidino-2-phenylindole<br />
|Nuclei<br />
|Incorporates into the DNA<br />
|[http://en.wikipedia.org/wiki/DAPI DAPI], [http://en.wikipedia.org/wiki/Hoechst_stain Hoechst]<br />
|-<br />
|PCNA<br />
|Proliferating-Cell-Nuclear-Antigen<br />
|Dividing cells<br />
|<br />
|[http://en.wikipedia.org/wiki/PCNA PCNA]<br />
|-<br />
|SOX2<br />
|SRY (sex determining region Y)-box 2<br />
|Preferentially neuronal lineage<br />
|Progenitor marker for both spinal cord and brain<br />
|[http://en.wikipedia.org/wiki/Sox2 SOX2]<br />
|-<br />
|PAX6<br />
|Paired box protein Pax-6<br />
|Brain/spinal cord<br />
|aka aniridia type II protein (AN2) or oculorhombin<br />
|[http://en.wikipedia.org/wiki/Pax6 PAX6]<br />
|-<br />
|PAX7<br />
|Paired box protein Pax-7<br />
|Satellite cells/spinal cord/brain<br />
|<br />
|[http://en.wikipedia.org/wiki/PAX7 PAX7]<br />
|-<br />
|MHC<br />
|Myosin heavy chain<br />
|Muscle fibers<br />
|<br />
|[http://en.wikipedia.org/wiki/Myosin_heavy_chain MHC]<br />
|-<br />
|MYF5<br />
|<br />
|Muscle fibers<br />
|Regulates muscle differentiation, labels cycling myoblasts<br />
|[http://en.wikipedia.org/wiki/Myf5 MYF5]<br />
|-<br />
|TUBB3<br />
|ßIII-tubulin<br />
|Axons<br />
|<br />
|[http://en.wikipedia.org/wiki/TUBB3 TUBB3]<br />
|-<br />
|MBP<br />
|Myelin basic protein<br />
|Schwann cells<br />
|<br />
|-<br />
|PRRX1<br />
|Paired mesoderm homeobox protein 1<br />
|Blastema/mesodermal cells of limb bud<br />
|<br />
|[http://en.wikipedia.org/wiki/PRRX1 PRRX1]<br />
|-<br />
|SMA<br />
|Smooth muscle actin<br />
|Blood vessels/endothelial cells<br />
|<br />
|<br />
|-<br />
|GFAP<br />
|Glial fibrillary acidic protein<br />
|Glia<br />
|<br />
|[http://en.wikipedia.org/wiki/Glial_fibrillary_acidic_protein GFAP]<br />
|-<br />
|NeuN<br />
|Feminizing Locus on X-3, Fox-3, or Hexaribonucleotide Binding Protein-3<br />
|Differentiated nerve<br />
|<br />
|[http://en.wikipedia.org/wiki/NeuN NeuN]<br />
|-<br />
|LEU7/HNK1/B3GAT1/CD57<br />
|Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 1<br />
|Schwann cells<br />
|<br />
|[http://en.wikipedia.org/wiki/B3GAT1 B3GAT1]<br />
|-<br />
|XBRA<br />
|Xbrachyury<br />
|Mesoderm during gastrula stage<br />
|<br />
|[http://en.wikipedia.org/wiki/Brachyury Brachyury]<br />
|-<br />
|MSX1<br />
|Muscle segment homeobox, Msh homeobox 1<br />
|Undifferentiated cells<br />
|Transcriptional repressor during embryogenesis<br />
|[http://en.wikipedia.org/wiki/MSX1 MSX1]<br />
|-<br />
|Trypan blue<br />
|<br />
|Dead tissues or cells<br />
|Vital stain<br />
|[http://en.wikipedia.org/wiki/Trypan_blue Trypan blue]<br />
|-<br />
|MEF2C<br />
|Myocyte-specific enhancer factor 2C<br />
|Differentiated muscle cells<br />
|aka MADS box transcription enhancer factor 2, polypeptide C<br />
|[http://en.wikipedia.org/wiki/Mef2c MEF2C]<br />
|-<br />
|PH3<br />
|Phosphine<br />
|Mitotic cells<br />
|<br />
|[http://en.wikipedia.org/wiki/Ph3 PH3]<br />
|-<br />
|BrdU<br />
|Bromodeoxyuridine<br />
|Cells in S-phase<br />
|<br />
|[http://en.wikipedia.org/wiki/Brdu BrdU]<br />
|-<br />
|CASP3<br />
|Caspase 3<br />
|Dying cells<br />
|<br />
|[http://en.wikipedia.org/wiki/CASP3 CASP3]<br />
|-<br />
|GDF5<br />
|Growth/differentiation factor 5<br />
|Joints<br />
|Joint development marker<br />
|[http://en.wikipedia.org/wiki/GDF5 GDF5]<br />
|-<br />
|Survivin<br />
|<br />
|Cleavage furrow<br />
|aka baculoviral inhibitor of apoptosis repeat-containing 5 or BIRC5<br />
|[http://en.wikipedia.org/wiki/Survivin Survivin]<br />
|-<br />
|MAP2<br />
|Microtubule-associated protein 2<br />
|Neurons<br />
|<br />
|[http://en.wikipedia.org/wiki/MAP2 MAP2]<br />
|-<br />
|SOX9<br />
|SRY (sex determining region Y)-box 2<br />
|Cartillage progenitors<br />
|<br />
|[http://en.wikipedia.org/wiki/Sox9 SOX9]<br />
|-<br />
|Rhodamine dextran<br />
|<br />
|Neurons<br />
|<br />
|<br />
|-<br />
|MBP<br />
|Myelin basic protein<br />
|Myelin sheath<br />
|<br />
|[http://en.wikipedia.org/wiki/Myelin_basic_protein MBP]<br />
|}<br />
<br />
== Digital data ==<br />
Over the years the members of the lab have produced a lot of different data: Sanger sequences, EST libraries, images and so on. <br />
Select a category from the list below in order to view or download the data.<br />
<br />
=== Fileservers ===<br />
{| class="wikitable"<br />
!style="width: 350px" | Location<br />
!style="width: 250px" | Volume size<br />
!style="width: 350px" | Description<br />
!style="width: 350px" | Access<br />
!style="width: 350px" | Location (console only)<br />
|-<br />
|//biodata/groups/<b>crtd_tanaka</b><br />
|16 TB<br />
|General purpose storage space<br />
|Entire Tanaka lab<br />
|<i>biocluster:</i> <b>/group/crtd_tanaka</b><br />
|-<br />
|//biodata/groups/<b>tanaka-ests</b><br />
|247 GB<br />
|EST sequences<br />
|Entire Tanaka lab<br />
|<i>biocluster:</i> <b>/group/tanaka-ests</b><br />
|-<br />
|//biodata/groups/<b>axolotl-transcriptome</b><br />
|500 GB<br />
|Axolotl transcriptome data<br />
|Elly, Sergej<br />
|<i>biocluster:</i> <b>/projects/axolotl-transcriptome</b><br />
|-<br />
|//biodata/groups/<b>tanaka-saori</b><br />
|878 GB<br />
|Special directory for Saori's data<br />
|Elly, Saori, Sergej<br />
|<i>biocluster:</i> <b>/group/tanaka-saori</b><br />
|}<br />
<br />
{{Tip|The path is different, when accessing the file server from the console.}}<br />
<br />
=== Literature ===<br />
<ul><br />
<li>[[Literature#Theses|Theses]]</li><br />
<li>[[Literature#Publications|Publications]]</li><br />
</ul><br />
<br />
=== Databases ===<br />
<ul><br />
<li>[http://est.age.mpg.de/axolotl/ Axolotl transcriptome] website contains the Axolotl transcriptome assemblies</li><br />
<li>[http://newtomics.mpi-bn.mpg.de/ Newt transcriptome] website contains the Newt transcriptome assembly</li><br />
<li>[http://sandberg.cmb.ki.se/redspottednewt/ Red spotted newt transcriptome] website contains the red spotted newt transcriptome assembly</li><br />
<li>[https://python-srv1.mpi-cbg.de/axolotl/cgi-bin/login.cgi Axolotl EST] database contains several ESTs and also some additional information, e.g. the position of the well with the corresponding insert in the Blastema (BL) or Neural tube (NT) library.</li><br />
<li>[http://est.age.mpg.de/ Axologle] database contains expression profiling data of Axolotl limb regeneration</li><br />
<li>[http://est.age.mpg.de/blast/blast.html Axolotl BLAST] database contains several different BLAST-able Axolotl transciptome assemblies</li><br />
</ul><br />
<br />
=== Datasets ===<br />
<ul><br />
<li>[[Datasets#Sequences|Sequences]]<br />
<ul><br />
<li>[[Datasets#Illumina|Illumina]]</li><br />
<li>[[Datasets#Sanger|Sanger]]</li><br />
<li>[[Datasets#Roche.2F454|Roche/454]]</li><br />
</ul><br />
</li><br />
<li>[[Datasets#Microarrays|Microarrays]]<br />
</ul><br />
<br />
=== Interesting links ===<br />
<ul><br />
<li>[http://www.nytimes.com/video/2013/02/27/science/100000002087758/finding-the-visible-in-the-invisible.html Visible in the invisible]: a movie introducing a new image processing ana analysis technique developed at the MIT.</li><br />
</ul><br />
<br />
== Lab life ==<br />
<ul><br />
<li>[[Lab_photos|Lab photos]]</li><br />
<li>Further pictures can be found in <b>/biodata/groups/crtd_tanaka/LabFun/</b></li><br />
<li>The recepies for Heino's farewell present can be found under <b>/biodata/groups/crtd_tanaka/LabFun/Heino's farewell present/</b></li><br />
<li>The video of the visit of the EU commissioner can be found under <b>/biodata/groups/crtd_tanaka/LabFun/</b></li><br />
</ul></div>
Serghein
https://wiki.tanakalab.org/index.php?title=Overview&diff=288
Overview
2013-07-16T14:18:54Z
<p>Serghein: /* Markers */</p>
<hr />
<div>== Introduction ==<br />
On the pages listed below you can find most common protocols used in the lab as well as a list of lab duties along with the names of the responsible persons. Please, contact the responsible persons if you have any question, suggestions or troubles.<br />
<br />
== Axolotl ==<br />
<br />
=== Maintainance ===<br />
In this section you will find some general information on how to [[Axolotl#Maintaining_the_axolotls|maintain]] the animals.<br />
<br />
=== Feeding ===<br />
This section will give you an overview of how to [[Axolotl#Feeding|feed]] the axolotls.<br />
<br />
=== Interesting observations ===<br />
In the following section you can find some [[Axolotl#Interesting_observations|interesting observations]] concerning the axolotl, its behavior, caveats of the transgenics and many more.<br />
<br />
== Lab duties ==<br />
<ul><br />
=== Chemicals ===<br />
<li>[[Antibiotics|Antibiotics]]</li><br />
<li>[[Benzocaine|Benzocaine]]</li><br />
<li>[[Fibronectin|Fibronectin]]</li><br />
<li>[[Gelatine|Gelatine]]</li><br />
<li>[[Liquid_nitrogen|Liquid nitrogen]]</li><br />
<li>[[Primary_antibodies|Primary antibodies]]</li><br />
<li>[[Secondary_antibodies|Secondary antibodies]]</li><br />
<li>[[Serum_immunostaining|Serum immunostaining]]</li><br />
<br />
=== Hardware ===<br />
<li>[[Autoclave|Autoclave]]</li><br />
<li>[[Cryostat|Cryostat]]</li><br />
<li>[[Dissecting_microscopes|Dissecting microscopes]]</li><br />
<li>[[Leica_confocal_microscope|Leica confocal microscope]]</li><br />
<li>[[Vacuum_pumps|Vacuum pumps]]</li><br />
<li>[[Waterbath|Waterbath]]</li><br />
<br />
=== General ===<br />
<li>[[Ordering_common_stuff|Ordering common stuff]]</li><br />
<li>[[Heat_shock_competent_cells|Heat-shock competent cells]]</li><br />
</ul><br />
<br />
<br />
== Protocols ==<br />
<ul><br />
=== Cell culture ===<br />
<li>[[Blastema_cells|Blastema cells]]</li><br />
<li>[[Baculovirus_titration|Baculovirus titration]]</li><br />
<li>[[Myoblasts_electroporation|Myoblasts electroporation]]</li><br />
<li>[[Adhesive_cell_culture|Adhesive cell culture]]</li><br />
<li>[[Electroporation_of_blastema_cells|Electroporation of blastema cells]]</li><br />
<li>[[Electroporation_of_nec|Electroporation of neural epithelia cells (axolotl spinal cord)]]</li><br />
<li>[[mESC_culture|mESC culture/Cyst formation]]</li><br />
<li>[[Neurosphere_culture|Neurosphere culture]]</li><br />
=== Histology ===<br />
<li>[[Double_Immunostaining_via_antigen_retrieval|Double Immunostaining via antigen retrieval (Sherry)]]</li><br />
=== Molecular biology ===<br />
<li>[[Metamorphosis_protocol|Metamorphosis protocol (Sherry)]]</li><br />
</ul><br />
<br />
== Booking calendars ==<br />
Since some pieces of hardware are used intensively it is necessary to book them in advance. The links to the corresponding booking calendars are listed below.<br />
<ul><br />
<li><br />
Fluorescence microscopes<br />
<ul><br />
<li>[http://www.my.calendars.net/olympusszx16 Olympus SZX 16]</li><br />
<li>[http://www.my.calendars.net/new_olympus/ New Olympus SZX 16]</li><br />
<li>[http://www.my.calendars.net/Olympus_OVK Olympus OVK]</li><br />
<li>[http://www.my.calendars.net/axio_observer/ Axio Observer]</li><br />
</ul><br />
</li><br />
<li><br />
Microinjectors and electroporators and dissecting microscope<br />
<ul><br />
<li>Room 0.232<br />
<ul> <br />
<li>[http://www.my.calendars.net/electroporator Nepa Gene]</li><br />
<li>[http://www.my.calendars.net/electroporator2 ECM 830]</li><br />
<li>[http://www.my.calendars.net/stereoscope2/d01/11/2012 Olympus dissecting microscope]</li><br />
</ul><br />
</li><br />
<li>Lab<br />
<ul><br />
<li>[http://www.my.calendars.net/OlympusLab Olympus (next to the axolotls)]</li><br />
<li>[http://www.my.calendars.net/OlympusLab2 Olympus (next to the Microtome)]</li><br />
</ul><br />
</li><br />
</ul><br />
</li><br />
<li><br />
Confocal microscopes<br />
<ul><br />
<li>[http://www.my.calendars.net/leica_lsm Leica LSM]</li><br />
</ul><br />
</li><br />
<li><br />
Cryostats<br />
<ul><br />
<li>[http://www.my.calendars.net/cryostat1 Cryostat 1]</li><br />
<li>[http://www.my.calendars.net/cryostat2 Cryostat 2]</li><br />
</ul><br />
</li><br />
<li><br />
Microtome<br />
<ul><br />
<li>[http://www.my.calendars.net/microtome Microtome]</li><br />
</ul><br />
</li><br />
<li><br />
Paraffin embedding station<br />
<ul><br />
<li>[http://www.my.calendars.net/wax_station Paraffin embedding station]</li><br />
</ul><br />
</li><br />
</ul><br />
<br />
== Genetics ==<br />
=== Transgenic lines ===<br />
<ul><br />
<li>[[Transgenic_axolotl_lines|Axolotl (A.mexicanum)]]</li><br />
<li>[[Transgenic_frog_lines|Frog (X.laevis)]]</li><br />
</ul><br />
<br />
=== Markers ===<br />
{| class="wikitable sortable"<br />
!style="width: 150px" | Marker<br />
!style="width: 250px" | Full name<br />
!style="width: 250px" | Target<br />
!style="width: 450px" | Remarks<br />
!style="width: 200px" | Link<br />
|-<br />
|DAPI/Hoechst<br />
|4',6-diamidino-2-phenylindole<br />
|Nuclei<br />
|Incorporates into the DNA<br />
|[http://en.wikipedia.org/wiki/DAPI DAPI], [http://en.wikipedia.org/wiki/Hoechst_stain Hoechst]<br />
|-<br />
|PCNA<br />
|Proliferating-Cell-Nuclear-Antigen<br />
|Dividing cells<br />
|<br />
|[http://en.wikipedia.org/wiki/PCNA PCNA]<br />
|-<br />
|SOX2<br />
|SRY (sex determining region Y)-box 2<br />
|Preferentially neuronal lineage<br />
|Progenitor marker for both spinal cord and brain<br />
|[http://en.wikipedia.org/wiki/Sox2 SOX2]<br />
|-<br />
|PAX6<br />
|Paired box protein Pax-6<br />
|Brain/spinal cord<br />
|aka aniridia type II protein (AN2) or oculorhombin<br />
|[http://en.wikipedia.org/wiki/Pax6 PAX6]<br />
|-<br />
|PAX7<br />
|Paired box protein Pax-7<br />
|Satellite cells/spinal cord/brain<br />
|<br />
|[http://en.wikipedia.org/wiki/PAX7 PAX7]<br />
|-<br />
|MHC<br />
|Myosin heavy chain<br />
|Muscle fibers<br />
|<br />
|[http://en.wikipedia.org/wiki/Myosin_heavy_chain MHC]<br />
|-<br />
|MYF5<br />
|<br />
|Muscle fibers<br />
|Regulates muscle differentiation, labels cycling myoblasts<br />
|[http://en.wikipedia.org/wiki/Myf5 MYF5]<br />
|-<br />
|TUBB3<br />
|ßIII-tubulin<br />
|Axons<br />
|<br />
|[http://en.wikipedia.org/wiki/TUBB3 TUBB3]<br />
|-<br />
|MBP<br />
|Myelin basic protein<br />
|Schwann cells<br />
|<br />
|-<br />
|PRRX1<br />
|Paired mesoderm homeobox protein 1<br />
|Blastema/mesodermal cells of limb bud<br />
|<br />
|[http://en.wikipedia.org/wiki/PRRX1 PRRX1]<br />
|-<br />
|SMA<br />
|Smooth muscle actin<br />
|Blood vessels/endothelial cells<br />
|<br />
|<br />
|-<br />
|GFAP<br />
|Glial fibrillary acidic protein<br />
|Glia<br />
|<br />
|[http://en.wikipedia.org/wiki/Glial_fibrillary_acidic_protein GFAP]<br />
|-<br />
|NeuN<br />
|Feminizing Locus on X-3, Fox-3, or Hexaribonucleotide Binding Protein-3<br />
|Differentiated nerve<br />
|<br />
|[http://en.wikipedia.org/wiki/NeuN NeuN]<br />
|-<br />
|LEU7/HNK1/B3GAT1/CD57<br />
|Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 1<br />
|Schwann cells<br />
|<br />
|[http://en.wikipedia.org/wiki/B3GAT1 B3GAT1]<br />
|-<br />
|XBRA<br />
|Xbrachyury<br />
|Mesoderm during gastrula stage<br />
|<br />
|[http://en.wikipedia.org/wiki/Brachyury Brachyury]<br />
|-<br />
|MSX1<br />
|Muscle segment homeobox, Msh homeobox 1<br />
|Undifferentiated cells<br />
|Transcriptional repressor during embryogenesis<br />
|[http://en.wikipedia.org/wiki/MSX1 MSX1]<br />
|-<br />
|Trypan blue<br />
|<br />
|Dead tissues or cells<br />
|Vital stain<br />
|[http://en.wikipedia.org/wiki/Trypan_blue Trypan blue]<br />
|-<br />
|MEF2C<br />
|Myocyte-specific enhancer factor 2C<br />
|Differentiated muscle cells<br />
|aka MADS box transcription enhancer factor 2, polypeptide C<br />
|[http://en.wikipedia.org/wiki/Mef2c MEF2C]<br />
|-<br />
|PH3<br />
|Phosphine<br />
|Mitotic cells<br />
|<br />
|[http://en.wikipedia.org/wiki/Ph3 PH3]<br />
|-<br />
|BrdU<br />
|Bromodeoxyuridine<br />
|Cells in S-phase<br />
|<br />
|[http://en.wikipedia.org/wiki/Brdu BrdU]<br />
|-<br />
|CASP3<br />
|Caspase 3<br />
|Dying cells<br />
|<br />
|[http://en.wikipedia.org/wiki/CASP3 CASP3]<br />
|-<br />
|GDF5<br />
|Growth/differentiation factor 5<br />
|Joints<br />
|Joint development marker<br />
|[http://en.wikipedia.org/wiki/GDF5 GDF5]<br />
|-<br />
|Survivin<br />
|<br />
|Cleavage furrow<br />
|aka baculoviral inhibitor of apoptosis repeat-containing 5 or BIRC5<br />
|[http://en.wikipedia.org/wiki/Survivin Survivin]<br />
|-<br />
|MAP2<br />
|Microtubule-associated protein 2<br />
|Neurons<br />
|<br />
|[http://en.wikipedia.org/wiki/MAP2 MAP2]<br />
|-<br />
|SOX9<br />
|SRY (sex determining region Y)-box 2<br />
|Cartillage progenitors<br />
|<br />
|[http://en.wikipedia.org/wiki/Sox9 SOX9]<br />
|-<br />
|Rhodamine dextran<br />
|<br />
|Neurons<br />
|<br />
|<br />
|-<br />
|MBP<br />
|Myelin basic protein<br />
|Neurons<br />
|<br />
|[http://en.wikipedia.org/wiki/Myelin_basic_protein MBP]<br />
|}<br />
<br />
== Digital data ==<br />
Over the years the members of the lab have produced a lot of different data: Sanger sequences, EST libraries, images and so on. <br />
Select a category from the list below in order to view or download the data.<br />
<br />
=== Fileservers ===<br />
{| class="wikitable"<br />
!style="width: 350px" | Location<br />
!style="width: 250px" | Volume size<br />
!style="width: 350px" | Description<br />
!style="width: 350px" | Access<br />
!style="width: 350px" | Location (console only)<br />
|-<br />
|//biodata/groups/<b>crtd_tanaka</b><br />
|16 TB<br />
|General purpose storage space<br />
|Entire Tanaka lab<br />
|<i>biocluster:</i> <b>/group/crtd_tanaka</b><br />
|-<br />
|//biodata/groups/<b>tanaka-ests</b><br />
|247 GB<br />
|EST sequences<br />
|Entire Tanaka lab<br />
|<i>biocluster:</i> <b>/group/tanaka-ests</b><br />
|-<br />
|//biodata/groups/<b>axolotl-transcriptome</b><br />
|500 GB<br />
|Axolotl transcriptome data<br />
|Elly, Sergej<br />
|<i>biocluster:</i> <b>/projects/axolotl-transcriptome</b><br />
|-<br />
|//biodata/groups/<b>tanaka-saori</b><br />
|878 GB<br />
|Special directory for Saori's data<br />
|Elly, Saori, Sergej<br />
|<i>biocluster:</i> <b>/group/tanaka-saori</b><br />
|}<br />
<br />
{{Tip|The path is different, when accessing the file server from the console.}}<br />
<br />
=== Literature ===<br />
<ul><br />
<li>[[Literature#Theses|Theses]]</li><br />
<li>[[Literature#Publications|Publications]]</li><br />
</ul><br />
<br />
=== Databases ===<br />
<ul><br />
<li>[http://est.age.mpg.de/axolotl/ Axolotl transcriptome] website contains the Axolotl transcriptome assemblies</li><br />
<li>[http://newtomics.mpi-bn.mpg.de/ Newt transcriptome] website contains the Newt transcriptome assembly</li><br />
<li>[http://sandberg.cmb.ki.se/redspottednewt/ Red spotted newt transcriptome] website contains the red spotted newt transcriptome assembly</li><br />
<li>[https://python-srv1.mpi-cbg.de/axolotl/cgi-bin/login.cgi Axolotl EST] database contains several ESTs and also some additional information, e.g. the position of the well with the corresponding insert in the Blastema (BL) or Neural tube (NT) library.</li><br />
<li>[http://est.age.mpg.de/ Axologle] database contains expression profiling data of Axolotl limb regeneration</li><br />
<li>[http://est.age.mpg.de/blast/blast.html Axolotl BLAST] database contains several different BLAST-able Axolotl transciptome assemblies</li><br />
</ul><br />
<br />
=== Datasets ===<br />
<ul><br />
<li>[[Datasets#Sequences|Sequences]]<br />
<ul><br />
<li>[[Datasets#Illumina|Illumina]]</li><br />
<li>[[Datasets#Sanger|Sanger]]</li><br />
<li>[[Datasets#Roche.2F454|Roche/454]]</li><br />
</ul><br />
</li><br />
<li>[[Datasets#Microarrays|Microarrays]]<br />
</ul><br />
<br />
=== Interesting links ===<br />
<ul><br />
<li>[http://www.nytimes.com/video/2013/02/27/science/100000002087758/finding-the-visible-in-the-invisible.html Visible in the invisible]: a movie introducing a new image processing ana analysis technique developed at the MIT.</li><br />
</ul><br />
<br />
== Lab life ==<br />
<ul><br />
<li>[[Lab_photos|Lab photos]]</li><br />
<li>Further pictures can be found in <b>/biodata/groups/crtd_tanaka/LabFun/</b></li><br />
<li>The recepies for Heino's farewell present can be found under <b>/biodata/groups/crtd_tanaka/LabFun/Heino's farewell present/</b></li><br />
<li>The video of the visit of the EU commissioner can be found under <b>/biodata/groups/crtd_tanaka/LabFun/</b></li><br />
</ul></div>
Serghein
https://wiki.tanakalab.org/index.php?title=Overview&diff=287
Overview
2013-07-16T14:06:15Z
<p>Serghein: /* Markers */</p>
<hr />
<div>== Introduction ==<br />
On the pages listed below you can find most common protocols used in the lab as well as a list of lab duties along with the names of the responsible persons. Please, contact the responsible persons if you have any question, suggestions or troubles.<br />
<br />
== Axolotl ==<br />
<br />
=== Maintainance ===<br />
In this section you will find some general information on how to [[Axolotl#Maintaining_the_axolotls|maintain]] the animals.<br />
<br />
=== Feeding ===<br />
This section will give you an overview of how to [[Axolotl#Feeding|feed]] the axolotls.<br />
<br />
=== Interesting observations ===<br />
In the following section you can find some [[Axolotl#Interesting_observations|interesting observations]] concerning the axolotl, its behavior, caveats of the transgenics and many more.<br />
<br />
== Lab duties ==<br />
<ul><br />
=== Chemicals ===<br />
<li>[[Antibiotics|Antibiotics]]</li><br />
<li>[[Benzocaine|Benzocaine]]</li><br />
<li>[[Fibronectin|Fibronectin]]</li><br />
<li>[[Gelatine|Gelatine]]</li><br />
<li>[[Liquid_nitrogen|Liquid nitrogen]]</li><br />
<li>[[Primary_antibodies|Primary antibodies]]</li><br />
<li>[[Secondary_antibodies|Secondary antibodies]]</li><br />
<li>[[Serum_immunostaining|Serum immunostaining]]</li><br />
<br />
=== Hardware ===<br />
<li>[[Autoclave|Autoclave]]</li><br />
<li>[[Cryostat|Cryostat]]</li><br />
<li>[[Dissecting_microscopes|Dissecting microscopes]]</li><br />
<li>[[Leica_confocal_microscope|Leica confocal microscope]]</li><br />
<li>[[Vacuum_pumps|Vacuum pumps]]</li><br />
<li>[[Waterbath|Waterbath]]</li><br />
<br />
=== General ===<br />
<li>[[Ordering_common_stuff|Ordering common stuff]]</li><br />
<li>[[Heat_shock_competent_cells|Heat-shock competent cells]]</li><br />
</ul><br />
<br />
<br />
== Protocols ==<br />
<ul><br />
=== Cell culture ===<br />
<li>[[Blastema_cells|Blastema cells]]</li><br />
<li>[[Baculovirus_titration|Baculovirus titration]]</li><br />
<li>[[Myoblasts_electroporation|Myoblasts electroporation]]</li><br />
<li>[[Adhesive_cell_culture|Adhesive cell culture]]</li><br />
<li>[[Electroporation_of_blastema_cells|Electroporation of blastema cells]]</li><br />
<li>[[Electroporation_of_nec|Electroporation of neural epithelia cells (axolotl spinal cord)]]</li><br />
<li>[[mESC_culture|mESC culture/Cyst formation]]</li><br />
<li>[[Neurosphere_culture|Neurosphere culture]]</li><br />
=== Histology ===<br />
<li>[[Double_Immunostaining_via_antigen_retrieval|Double Immunostaining via antigen retrieval (Sherry)]]</li><br />
=== Molecular biology ===<br />
<li>[[Metamorphosis_protocol|Metamorphosis protocol (Sherry)]]</li><br />
</ul><br />
<br />
== Booking calendars ==<br />
Since some pieces of hardware are used intensively it is necessary to book them in advance. The links to the corresponding booking calendars are listed below.<br />
<ul><br />
<li><br />
Fluorescence microscopes<br />
<ul><br />
<li>[http://www.my.calendars.net/olympusszx16 Olympus SZX 16]</li><br />
<li>[http://www.my.calendars.net/new_olympus/ New Olympus SZX 16]</li><br />
<li>[http://www.my.calendars.net/Olympus_OVK Olympus OVK]</li><br />
<li>[http://www.my.calendars.net/axio_observer/ Axio Observer]</li><br />
</ul><br />
</li><br />
<li><br />
Microinjectors and electroporators and dissecting microscope<br />
<ul><br />
<li>Room 0.232<br />
<ul> <br />
<li>[http://www.my.calendars.net/electroporator Nepa Gene]</li><br />
<li>[http://www.my.calendars.net/electroporator2 ECM 830]</li><br />
<li>[http://www.my.calendars.net/stereoscope2/d01/11/2012 Olympus dissecting microscope]</li><br />
</ul><br />
</li><br />
<li>Lab<br />
<ul><br />
<li>[http://www.my.calendars.net/OlympusLab Olympus (next to the axolotls)]</li><br />
<li>[http://www.my.calendars.net/OlympusLab2 Olympus (next to the Microtome)]</li><br />
</ul><br />
</li><br />
</ul><br />
</li><br />
<li><br />
Confocal microscopes<br />
<ul><br />
<li>[http://www.my.calendars.net/leica_lsm Leica LSM]</li><br />
</ul><br />
</li><br />
<li><br />
Cryostats<br />
<ul><br />
<li>[http://www.my.calendars.net/cryostat1 Cryostat 1]</li><br />
<li>[http://www.my.calendars.net/cryostat2 Cryostat 2]</li><br />
</ul><br />
</li><br />
<li><br />
Microtome<br />
<ul><br />
<li>[http://www.my.calendars.net/microtome Microtome]</li><br />
</ul><br />
</li><br />
<li><br />
Paraffin embedding station<br />
<ul><br />
<li>[http://www.my.calendars.net/wax_station Paraffin embedding station]</li><br />
</ul><br />
</li><br />
</ul><br />
<br />
== Genetics ==<br />
=== Transgenic lines ===<br />
<ul><br />
<li>[[Transgenic_axolotl_lines|Axolotl (A.mexicanum)]]</li><br />
<li>[[Transgenic_frog_lines|Frog (X.laevis)]]</li><br />
</ul><br />
<br />
=== Markers ===<br />
{| class="wikitable sortable"<br />
!style="width: 150px" | Marker<br />
!style="width: 250px" | Full name<br />
!style="width: 250px" | Target<br />
!style="width: 450px" | Remarks<br />
!style="width: 200px" | Link<br />
|-<br />
|DAPI/Hoechst<br />
|4',6-diamidino-2-phenylindole<br />
|Nuclei<br />
|Incorporates into the DNA<br />
|[http://en.wikipedia.org/wiki/DAPI DAPI], [http://en.wikipedia.org/wiki/Hoechst_stain Hoechst]<br />
|-<br />
|PCNA<br />
|Proliferating-Cell-Nuclear-Antigen<br />
|Dividing cells<br />
|<br />
|[http://en.wikipedia.org/wiki/PCNA PCNA]<br />
|-<br />
|SOX2<br />
|SRY (sex determining region Y)-box 2<br />
|Preferentially neuronal lineage<br />
|Progenitor marker for both spinal cord and brain<br />
|[http://en.wikipedia.org/wiki/Sox2 SOX2]<br />
|-<br />
|PAX6<br />
|Paired box protein Pax-6<br />
|Brain/spinal cord<br />
|aka aniridia type II protein (AN2) or oculorhombin<br />
|[http://en.wikipedia.org/wiki/Pax6 PAX6]<br />
|-<br />
|PAX7<br />
|Paired box protein Pax-7<br />
|Satellite cells/spinal cord/brain<br />
|<br />
|[http://en.wikipedia.org/wiki/PAX7 PAX7]<br />
|-<br />
|MHC<br />
|Myosin heavy chain<br />
|Muscle fibers<br />
|<br />
|[http://en.wikipedia.org/wiki/Myosin_heavy_chain MHC]<br />
|-<br />
|MYF5<br />
|<br />
|Muscle fibers<br />
|Regulates muscle differentiation, labels cycling myoblasts<br />
|[http://en.wikipedia.org/wiki/Myf5 MYF5]<br />
|-<br />
|TUBB3<br />
|ßIII-tubulin<br />
|Axons<br />
|<br />
|[http://en.wikipedia.org/wiki/TUBB3 TUBB3]<br />
|-<br />
|MBP<br />
|Myelin basic protein<br />
|Schwann cells<br />
|<br />
|-<br />
|PRRX1<br />
|Paired mesoderm homeobox protein 1<br />
|Blastema/mesodermal cells of limb bud<br />
|<br />
|[http://en.wikipedia.org/wiki/PRRX1 PRRX1]<br />
|-<br />
|SMA<br />
|Smooth muscle actin<br />
|Blood vessels/endothelial cells<br />
|<br />
|<br />
|-<br />
|GFAP<br />
|Glial fibrillary acidic protein<br />
|Glia<br />
|<br />
|[http://en.wikipedia.org/wiki/Glial_fibrillary_acidic_protein GFAP]<br />
|-<br />
|NeuN<br />
|Feminizing Locus on X-3, Fox-3, or Hexaribonucleotide Binding Protein-3<br />
|Differentiated nerve<br />
|<br />
|[http://en.wikipedia.org/wiki/NeuN NeuN]<br />
|-<br />
|LEU7/HNK1/B3GAT1/CD57<br />
|Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 1<br />
|Schwann cells<br />
|<br />
|[http://en.wikipedia.org/wiki/B3GAT1 B3GAT1]<br />
|-<br />
|XBRA<br />
|Xbrachyury<br />
|Mesoderm during gastrula stage<br />
|<br />
|[http://en.wikipedia.org/wiki/Brachyury Brachyury]<br />
|-<br />
|MSX1<br />
|Muscle segment homeobox, Msh homeobox 1<br />
|Undifferentiated cells<br />
|Transcriptional repressor during embryogenesis<br />
|[http://en.wikipedia.org/wiki/MSX1 MSX1]<br />
|-<br />
|Trypan blue<br />
|<br />
|Dead tissues or cells<br />
|Vital stain<br />
|[http://en.wikipedia.org/wiki/Trypan_blue Trypan blue]<br />
|-<br />
|MEF2C<br />
|Myocyte-specific enhancer factor 2C<br />
|Differentiated muscle cells<br />
|aka MADS box transcription enhancer factor 2, polypeptide C<br />
|[http://en.wikipedia.org/wiki/Mef2c MEF2C]<br />
|-<br />
|PH3<br />
|Phosphine<br />
|Mitotic cells<br />
|<br />
|[http://en.wikipedia.org/wiki/Ph3 PH3]<br />
|-<br />
|BrdU<br />
|Bromodeoxyuridine<br />
|Cells in S-phase<br />
|<br />
|[http://en.wikipedia.org/wiki/Brdu BrdU]<br />
|-<br />
|CASP3<br />
|Caspase 3<br />
|Dying cells<br />
|<br />
|[http://en.wikipedia.org/wiki/CASP3 CASP3]<br />
|-<br />
|GDF5<br />
|Growth/differentiation factor 5<br />
|Joints<br />
|Joint development marker<br />
|[http://en.wikipedia.org/wiki/GDF5 GDF5]<br />
|-<br />
|Survivin<br />
|<br />
|Cleavage furrow<br />
|aka baculoviral inhibitor of apoptosis repeat-containing 5 or BIRC5<br />
|[http://en.wikipedia.org/wiki/Survivin Survivin]<br />
|-<br />
|MAP2<br />
|Microtubule-associated protein 2<br />
|Neurons<br />
|<br />
|[http://en.wikipedia.org/wiki/MAP2 MAP2]<br />
|-<br />
|SOX9<br />
|SRY (sex determining region Y)-box 2<br />
|Cartillage progenitors<br />
|<br />
|[http://en.wikipedia.org/wiki/Sox9 SOX9]<br />
|-<br />
|Rhodamine dextran<br />
|<br />
|Neurons<br />
|<br />
|<br />
|}<br />
<br />
== Digital data ==<br />
Over the years the members of the lab have produced a lot of different data: Sanger sequences, EST libraries, images and so on. <br />
Select a category from the list below in order to view or download the data.<br />
<br />
=== Fileservers ===<br />
{| class="wikitable"<br />
!style="width: 350px" | Location<br />
!style="width: 250px" | Volume size<br />
!style="width: 350px" | Description<br />
!style="width: 350px" | Access<br />
!style="width: 350px" | Location (console only)<br />
|-<br />
|//biodata/groups/<b>crtd_tanaka</b><br />
|16 TB<br />
|General purpose storage space<br />
|Entire Tanaka lab<br />
|<i>biocluster:</i> <b>/group/crtd_tanaka</b><br />
|-<br />
|//biodata/groups/<b>tanaka-ests</b><br />
|247 GB<br />
|EST sequences<br />
|Entire Tanaka lab<br />
|<i>biocluster:</i> <b>/group/tanaka-ests</b><br />
|-<br />
|//biodata/groups/<b>axolotl-transcriptome</b><br />
|500 GB<br />
|Axolotl transcriptome data<br />
|Elly, Sergej<br />
|<i>biocluster:</i> <b>/projects/axolotl-transcriptome</b><br />
|-<br />
|//biodata/groups/<b>tanaka-saori</b><br />
|878 GB<br />
|Special directory for Saori's data<br />
|Elly, Saori, Sergej<br />
|<i>biocluster:</i> <b>/group/tanaka-saori</b><br />
|}<br />
<br />
{{Tip|The path is different, when accessing the file server from the console.}}<br />
<br />
=== Literature ===<br />
<ul><br />
<li>[[Literature#Theses|Theses]]</li><br />
<li>[[Literature#Publications|Publications]]</li><br />
</ul><br />
<br />
=== Databases ===<br />
<ul><br />
<li>[http://est.age.mpg.de/axolotl/ Axolotl transcriptome] website contains the Axolotl transcriptome assemblies</li><br />
<li>[http://newtomics.mpi-bn.mpg.de/ Newt transcriptome] website contains the Newt transcriptome assembly</li><br />
<li>[http://sandberg.cmb.ki.se/redspottednewt/ Red spotted newt transcriptome] website contains the red spotted newt transcriptome assembly</li><br />
<li>[https://python-srv1.mpi-cbg.de/axolotl/cgi-bin/login.cgi Axolotl EST] database contains several ESTs and also some additional information, e.g. the position of the well with the corresponding insert in the Blastema (BL) or Neural tube (NT) library.</li><br />
<li>[http://est.age.mpg.de/ Axologle] database contains expression profiling data of Axolotl limb regeneration</li><br />
<li>[http://est.age.mpg.de/blast/blast.html Axolotl BLAST] database contains several different BLAST-able Axolotl transciptome assemblies</li><br />
</ul><br />
<br />
=== Datasets ===<br />
<ul><br />
<li>[[Datasets#Sequences|Sequences]]<br />
<ul><br />
<li>[[Datasets#Illumina|Illumina]]</li><br />
<li>[[Datasets#Sanger|Sanger]]</li><br />
<li>[[Datasets#Roche.2F454|Roche/454]]</li><br />
</ul><br />
</li><br />
<li>[[Datasets#Microarrays|Microarrays]]<br />
</ul><br />
<br />
=== Interesting links ===<br />
<ul><br />
<li>[http://www.nytimes.com/video/2013/02/27/science/100000002087758/finding-the-visible-in-the-invisible.html Visible in the invisible]: a movie introducing a new image processing ana analysis technique developed at the MIT.</li><br />
</ul><br />
<br />
== Lab life ==<br />
<ul><br />
<li>[[Lab_photos|Lab photos]]</li><br />
<li>Further pictures can be found in <b>/biodata/groups/crtd_tanaka/LabFun/</b></li><br />
<li>The recepies for Heino's farewell present can be found under <b>/biodata/groups/crtd_tanaka/LabFun/Heino's farewell present/</b></li><br />
<li>The video of the visit of the EU commissioner can be found under <b>/biodata/groups/crtd_tanaka/LabFun/</b></li><br />
</ul></div>
Serghein
https://wiki.tanakalab.org/index.php?title=Overview&diff=286
Overview
2013-07-16T13:58:04Z
<p>Serghein: /* Markers */</p>
<hr />
<div>== Introduction ==<br />
On the pages listed below you can find most common protocols used in the lab as well as a list of lab duties along with the names of the responsible persons. Please, contact the responsible persons if you have any question, suggestions or troubles.<br />
<br />
== Axolotl ==<br />
<br />
=== Maintainance ===<br />
In this section you will find some general information on how to [[Axolotl#Maintaining_the_axolotls|maintain]] the animals.<br />
<br />
=== Feeding ===<br />
This section will give you an overview of how to [[Axolotl#Feeding|feed]] the axolotls.<br />
<br />
=== Interesting observations ===<br />
In the following section you can find some [[Axolotl#Interesting_observations|interesting observations]] concerning the axolotl, its behavior, caveats of the transgenics and many more.<br />
<br />
== Lab duties ==<br />
<ul><br />
=== Chemicals ===<br />
<li>[[Antibiotics|Antibiotics]]</li><br />
<li>[[Benzocaine|Benzocaine]]</li><br />
<li>[[Fibronectin|Fibronectin]]</li><br />
<li>[[Gelatine|Gelatine]]</li><br />
<li>[[Liquid_nitrogen|Liquid nitrogen]]</li><br />
<li>[[Primary_antibodies|Primary antibodies]]</li><br />
<li>[[Secondary_antibodies|Secondary antibodies]]</li><br />
<li>[[Serum_immunostaining|Serum immunostaining]]</li><br />
<br />
=== Hardware ===<br />
<li>[[Autoclave|Autoclave]]</li><br />
<li>[[Cryostat|Cryostat]]</li><br />
<li>[[Dissecting_microscopes|Dissecting microscopes]]</li><br />
<li>[[Leica_confocal_microscope|Leica confocal microscope]]</li><br />
<li>[[Vacuum_pumps|Vacuum pumps]]</li><br />
<li>[[Waterbath|Waterbath]]</li><br />
<br />
=== General ===<br />
<li>[[Ordering_common_stuff|Ordering common stuff]]</li><br />
<li>[[Heat_shock_competent_cells|Heat-shock competent cells]]</li><br />
</ul><br />
<br />
<br />
== Protocols ==<br />
<ul><br />
=== Cell culture ===<br />
<li>[[Blastema_cells|Blastema cells]]</li><br />
<li>[[Baculovirus_titration|Baculovirus titration]]</li><br />
<li>[[Myoblasts_electroporation|Myoblasts electroporation]]</li><br />
<li>[[Adhesive_cell_culture|Adhesive cell culture]]</li><br />
<li>[[Electroporation_of_blastema_cells|Electroporation of blastema cells]]</li><br />
<li>[[Electroporation_of_nec|Electroporation of neural epithelia cells (axolotl spinal cord)]]</li><br />
<li>[[mESC_culture|mESC culture/Cyst formation]]</li><br />
<li>[[Neurosphere_culture|Neurosphere culture]]</li><br />
=== Histology ===<br />
<li>[[Double_Immunostaining_via_antigen_retrieval|Double Immunostaining via antigen retrieval (Sherry)]]</li><br />
=== Molecular biology ===<br />
<li>[[Metamorphosis_protocol|Metamorphosis protocol (Sherry)]]</li><br />
</ul><br />
<br />
== Booking calendars ==<br />
Since some pieces of hardware are used intensively it is necessary to book them in advance. The links to the corresponding booking calendars are listed below.<br />
<ul><br />
<li><br />
Fluorescence microscopes<br />
<ul><br />
<li>[http://www.my.calendars.net/olympusszx16 Olympus SZX 16]</li><br />
<li>[http://www.my.calendars.net/new_olympus/ New Olympus SZX 16]</li><br />
<li>[http://www.my.calendars.net/Olympus_OVK Olympus OVK]</li><br />
<li>[http://www.my.calendars.net/axio_observer/ Axio Observer]</li><br />
</ul><br />
</li><br />
<li><br />
Microinjectors and electroporators and dissecting microscope<br />
<ul><br />
<li>Room 0.232<br />
<ul> <br />
<li>[http://www.my.calendars.net/electroporator Nepa Gene]</li><br />
<li>[http://www.my.calendars.net/electroporator2 ECM 830]</li><br />
<li>[http://www.my.calendars.net/stereoscope2/d01/11/2012 Olympus dissecting microscope]</li><br />
</ul><br />
</li><br />
<li>Lab<br />
<ul><br />
<li>[http://www.my.calendars.net/OlympusLab Olympus (next to the axolotls)]</li><br />
<li>[http://www.my.calendars.net/OlympusLab2 Olympus (next to the Microtome)]</li><br />
</ul><br />
</li><br />
</ul><br />
</li><br />
<li><br />
Confocal microscopes<br />
<ul><br />
<li>[http://www.my.calendars.net/leica_lsm Leica LSM]</li><br />
</ul><br />
</li><br />
<li><br />
Cryostats<br />
<ul><br />
<li>[http://www.my.calendars.net/cryostat1 Cryostat 1]</li><br />
<li>[http://www.my.calendars.net/cryostat2 Cryostat 2]</li><br />
</ul><br />
</li><br />
<li><br />
Microtome<br />
<ul><br />
<li>[http://www.my.calendars.net/microtome Microtome]</li><br />
</ul><br />
</li><br />
<li><br />
Paraffin embedding station<br />
<ul><br />
<li>[http://www.my.calendars.net/wax_station Paraffin embedding station]</li><br />
</ul><br />
</li><br />
</ul><br />
<br />
== Genetics ==<br />
=== Transgenic lines ===<br />
<ul><br />
<li>[[Transgenic_axolotl_lines|Axolotl (A.mexicanum)]]</li><br />
<li>[[Transgenic_frog_lines|Frog (X.laevis)]]</li><br />
</ul><br />
<br />
=== Markers ===<br />
{| class="wikitable sortable"<br />
!style="width: 150px" | Marker<br />
!style="width: 250px" | Full name<br />
!style="width: 250px" | Target<br />
!style="width: 450px" | Remarks<br />
!style="width: 200px" | Link<br />
|-<br />
|DAPI/Hoechst<br />
|4',6-diamidino-2-phenylindole<br />
|Nuclei<br />
|Incorporates into the DNA<br />
|[http://en.wikipedia.org/wiki/DAPI DAPI], [http://en.wikipedia.org/wiki/Hoechst_stain Hoechst]<br />
|-<br />
|PCNA<br />
|Proliferating-Cell-Nuclear-Antigen<br />
|Dividing cells<br />
|<br />
|[http://en.wikipedia.org/wiki/PCNA PCNA]<br />
|-<br />
|SOX2<br />
|SRY (sex determining region Y)-box 2<br />
|Preferentially neuronal lineage<br />
|Progenitor marker for both spinal cord and brain<br />
|[http://en.wikipedia.org/wiki/Sox2 SOX2]<br />
|-<br />
|PAX6<br />
|Paired box protein Pax-6<br />
|Brain/spinal cord<br />
|aka aniridia type II protein (AN2) or oculorhombin<br />
|[http://en.wikipedia.org/wiki/Pax6 PAX6]<br />
|-<br />
|PAX7<br />
|Paired box protein Pax-7<br />
|Satellite cells/spinal cord/brain<br />
|<br />
|[http://en.wikipedia.org/wiki/PAX7 PAX7]<br />
|-<br />
|MHC<br />
|Myosin heavy chain<br />
|Muscle fibers<br />
|<br />
|[http://en.wikipedia.org/wiki/Myosin_heavy_chain MHC]<br />
|-<br />
|MYF5<br />
|<br />
|Muscle fibers<br />
|Regulates muscle differentiation, labels cycling myoblasts<br />
|[http://en.wikipedia.org/wiki/Myf5 MYF5]<br />
|-<br />
|TUBB3<br />
|ßIII-tubulin<br />
|Axons<br />
|<br />
|[http://en.wikipedia.org/wiki/TUBB3 TUBB3]<br />
|-<br />
|MBP<br />
|Myelin basic protein<br />
|Schwann cells<br />
|<br />
|-<br />
|PRRX1<br />
|Paired mesoderm homeobox protein 1<br />
|Blastema/mesodermal cells of limb bud<br />
|<br />
|[http://en.wikipedia.org/wiki/PRRX1 PRRX1]<br />
|-<br />
|SMA<br />
|Smooth muscle actin<br />
|Blood vessels/endothelial cells<br />
|<br />
|<br />
|-<br />
|GFAP<br />
|Glial fibrillary acidic protein<br />
|Glia<br />
|<br />
|[http://en.wikipedia.org/wiki/Glial_fibrillary_acidic_protein GFAP]<br />
|-<br />
|NeuN<br />
|Feminizing Locus on X-3, Fox-3, or Hexaribonucleotide Binding Protein-3<br />
|Differentiated nerve<br />
|<br />
|[http://en.wikipedia.org/wiki/NeuN NeuN]<br />
|-<br />
|LEU7/HNK1/B3GAT1/CD57<br />
|Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 1<br />
|Schwann cells<br />
|<br />
|[http://en.wikipedia.org/wiki/B3GAT1 B3GAT1]<br />
|-<br />
|XBRA<br />
|Xbrachyury<br />
|Mesoderm during gastrula stage<br />
|<br />
|[http://en.wikipedia.org/wiki/Brachyury Brachyury]<br />
|-<br />
|MSX1<br />
|Muscle segment homeobox, Msh homeobox 1<br />
|Undifferentiated cells<br />
|Transcriptional repressor during embryogenesis<br />
|[http://en.wikipedia.org/wiki/MSX1 MSX1]<br />
|-<br />
|Trypan blue<br />
|<br />
|Dead tissues or cells<br />
|Vital stain<br />
|[http://en.wikipedia.org/wiki/Trypan_blue Trypan blue]<br />
|-<br />
|MEF2C<br />
|Myocyte-specific enhancer factor 2C<br />
|Differentiated muscle cells<br />
|aka MADS box transcription enhancer factor 2, polypeptide C<br />
|[http://en.wikipedia.org/wiki/Mef2c MEF2C]<br />
|-<br />
|PH3<br />
|Phosphine<br />
|Mitotic cells<br />
|<br />
|[http://en.wikipedia.org/wiki/Ph3 PH3]<br />
|-<br />
|BrdU<br />
|Bromodeoxyuridine<br />
|Cells in S-phase<br />
|<br />
|[http://en.wikipedia.org/wiki/Brdu BrdU]<br />
|-<br />
|CASP3<br />
|Caspase 3<br />
|Dying cells<br />
|<br />
|[http://en.wikipedia.org/wiki/CASP3 CASP3]<br />
|-<br />
|GDF5<br />
|Growth/differentiation factor 5<br />
|Joints<br />
|Joint development marker<br />
|[http://en.wikipedia.org/wiki/GDF5 GDF5]<br />
|-<br />
|Survivin<br />
|<br />
|Cleavage furrow<br />
|aka baculoviral inhibitor of apoptosis repeat-containing 5 or BIRC5<br />
|[http://en.wikipedia.org/wiki/Survivin Survivin]<br />
|-<br />
|MAP2<br />
|Microtubule-associated protein 2<br />
|Neurons<br />
|<br />
|[http://en.wikipedia.org/wiki/MAP2 MAP2]<br />
|-<br />
|SOX9<br />
|SRY (sex determining region Y)-box 2<br />
|Cartillage progenitors<br />
|<br />
|[http://en.wikipedia.org/wiki/Sox9 SOX9]<br />
|}<br />
<br />
== Digital data ==<br />
Over the years the members of the lab have produced a lot of different data: Sanger sequences, EST libraries, images and so on. <br />
Select a category from the list below in order to view or download the data.<br />
<br />
=== Fileservers ===<br />
{| class="wikitable"<br />
!style="width: 350px" | Location<br />
!style="width: 250px" | Volume size<br />
!style="width: 350px" | Description<br />
!style="width: 350px" | Access<br />
!style="width: 350px" | Location (console only)<br />
|-<br />
|//biodata/groups/<b>crtd_tanaka</b><br />
|16 TB<br />
|General purpose storage space<br />
|Entire Tanaka lab<br />
|<i>biocluster:</i> <b>/group/crtd_tanaka</b><br />
|-<br />
|//biodata/groups/<b>tanaka-ests</b><br />
|247 GB<br />
|EST sequences<br />
|Entire Tanaka lab<br />
|<i>biocluster:</i> <b>/group/tanaka-ests</b><br />
|-<br />
|//biodata/groups/<b>axolotl-transcriptome</b><br />
|500 GB<br />
|Axolotl transcriptome data<br />
|Elly, Sergej<br />
|<i>biocluster:</i> <b>/projects/axolotl-transcriptome</b><br />
|-<br />
|//biodata/groups/<b>tanaka-saori</b><br />
|878 GB<br />
|Special directory for Saori's data<br />
|Elly, Saori, Sergej<br />
|<i>biocluster:</i> <b>/group/tanaka-saori</b><br />
|}<br />
<br />
{{Tip|The path is different, when accessing the file server from the console.}}<br />
<br />
=== Literature ===<br />
<ul><br />
<li>[[Literature#Theses|Theses]]</li><br />
<li>[[Literature#Publications|Publications]]</li><br />
</ul><br />
<br />
=== Databases ===<br />
<ul><br />
<li>[http://est.age.mpg.de/axolotl/ Axolotl transcriptome] website contains the Axolotl transcriptome assemblies</li><br />
<li>[http://newtomics.mpi-bn.mpg.de/ Newt transcriptome] website contains the Newt transcriptome assembly</li><br />
<li>[http://sandberg.cmb.ki.se/redspottednewt/ Red spotted newt transcriptome] website contains the red spotted newt transcriptome assembly</li><br />
<li>[https://python-srv1.mpi-cbg.de/axolotl/cgi-bin/login.cgi Axolotl EST] database contains several ESTs and also some additional information, e.g. the position of the well with the corresponding insert in the Blastema (BL) or Neural tube (NT) library.</li><br />
<li>[http://est.age.mpg.de/ Axologle] database contains expression profiling data of Axolotl limb regeneration</li><br />
<li>[http://est.age.mpg.de/blast/blast.html Axolotl BLAST] database contains several different BLAST-able Axolotl transciptome assemblies</li><br />
</ul><br />
<br />
=== Datasets ===<br />
<ul><br />
<li>[[Datasets#Sequences|Sequences]]<br />
<ul><br />
<li>[[Datasets#Illumina|Illumina]]</li><br />
<li>[[Datasets#Sanger|Sanger]]</li><br />
<li>[[Datasets#Roche.2F454|Roche/454]]</li><br />
</ul><br />
</li><br />
<li>[[Datasets#Microarrays|Microarrays]]<br />
</ul><br />
<br />
=== Interesting links ===<br />
<ul><br />
<li>[http://www.nytimes.com/video/2013/02/27/science/100000002087758/finding-the-visible-in-the-invisible.html Visible in the invisible]: a movie introducing a new image processing ana analysis technique developed at the MIT.</li><br />
</ul><br />
<br />
== Lab life ==<br />
<ul><br />
<li>[[Lab_photos|Lab photos]]</li><br />
<li>Further pictures can be found in <b>/biodata/groups/crtd_tanaka/LabFun/</b></li><br />
<li>The recepies for Heino's farewell present can be found under <b>/biodata/groups/crtd_tanaka/LabFun/Heino's farewell present/</b></li><br />
<li>The video of the visit of the EU commissioner can be found under <b>/biodata/groups/crtd_tanaka/LabFun/</b></li><br />
</ul></div>
Serghein
https://wiki.tanakalab.org/index.php?title=Overview&diff=285
Overview
2013-07-16T13:34:36Z
<p>Serghein: /* Markers */</p>
<hr />
<div>== Introduction ==<br />
On the pages listed below you can find most common protocols used in the lab as well as a list of lab duties along with the names of the responsible persons. Please, contact the responsible persons if you have any question, suggestions or troubles.<br />
<br />
== Axolotl ==<br />
<br />
=== Maintainance ===<br />
In this section you will find some general information on how to [[Axolotl#Maintaining_the_axolotls|maintain]] the animals.<br />
<br />
=== Feeding ===<br />
This section will give you an overview of how to [[Axolotl#Feeding|feed]] the axolotls.<br />
<br />
=== Interesting observations ===<br />
In the following section you can find some [[Axolotl#Interesting_observations|interesting observations]] concerning the axolotl, its behavior, caveats of the transgenics and many more.<br />
<br />
== Lab duties ==<br />
<ul><br />
=== Chemicals ===<br />
<li>[[Antibiotics|Antibiotics]]</li><br />
<li>[[Benzocaine|Benzocaine]]</li><br />
<li>[[Fibronectin|Fibronectin]]</li><br />
<li>[[Gelatine|Gelatine]]</li><br />
<li>[[Liquid_nitrogen|Liquid nitrogen]]</li><br />
<li>[[Primary_antibodies|Primary antibodies]]</li><br />
<li>[[Secondary_antibodies|Secondary antibodies]]</li><br />
<li>[[Serum_immunostaining|Serum immunostaining]]</li><br />
<br />
=== Hardware ===<br />
<li>[[Autoclave|Autoclave]]</li><br />
<li>[[Cryostat|Cryostat]]</li><br />
<li>[[Dissecting_microscopes|Dissecting microscopes]]</li><br />
<li>[[Leica_confocal_microscope|Leica confocal microscope]]</li><br />
<li>[[Vacuum_pumps|Vacuum pumps]]</li><br />
<li>[[Waterbath|Waterbath]]</li><br />
<br />
=== General ===<br />
<li>[[Ordering_common_stuff|Ordering common stuff]]</li><br />
<li>[[Heat_shock_competent_cells|Heat-shock competent cells]]</li><br />
</ul><br />
<br />
<br />
== Protocols ==<br />
<ul><br />
=== Cell culture ===<br />
<li>[[Blastema_cells|Blastema cells]]</li><br />
<li>[[Baculovirus_titration|Baculovirus titration]]</li><br />
<li>[[Myoblasts_electroporation|Myoblasts electroporation]]</li><br />
<li>[[Adhesive_cell_culture|Adhesive cell culture]]</li><br />
<li>[[Electroporation_of_blastema_cells|Electroporation of blastema cells]]</li><br />
<li>[[Electroporation_of_nec|Electroporation of neural epithelia cells (axolotl spinal cord)]]</li><br />
<li>[[mESC_culture|mESC culture/Cyst formation]]</li><br />
<li>[[Neurosphere_culture|Neurosphere culture]]</li><br />
=== Histology ===<br />
<li>[[Double_Immunostaining_via_antigen_retrieval|Double Immunostaining via antigen retrieval (Sherry)]]</li><br />
=== Molecular biology ===<br />
<li>[[Metamorphosis_protocol|Metamorphosis protocol (Sherry)]]</li><br />
</ul><br />
<br />
== Booking calendars ==<br />
Since some pieces of hardware are used intensively it is necessary to book them in advance. The links to the corresponding booking calendars are listed below.<br />
<ul><br />
<li><br />
Fluorescence microscopes<br />
<ul><br />
<li>[http://www.my.calendars.net/olympusszx16 Olympus SZX 16]</li><br />
<li>[http://www.my.calendars.net/new_olympus/ New Olympus SZX 16]</li><br />
<li>[http://www.my.calendars.net/Olympus_OVK Olympus OVK]</li><br />
<li>[http://www.my.calendars.net/axio_observer/ Axio Observer]</li><br />
</ul><br />
</li><br />
<li><br />
Microinjectors and electroporators and dissecting microscope<br />
<ul><br />
<li>Room 0.232<br />
<ul> <br />
<li>[http://www.my.calendars.net/electroporator Nepa Gene]</li><br />
<li>[http://www.my.calendars.net/electroporator2 ECM 830]</li><br />
<li>[http://www.my.calendars.net/stereoscope2/d01/11/2012 Olympus dissecting microscope]</li><br />
</ul><br />
</li><br />
<li>Lab<br />
<ul><br />
<li>[http://www.my.calendars.net/OlympusLab Olympus (next to the axolotls)]</li><br />
<li>[http://www.my.calendars.net/OlympusLab2 Olympus (next to the Microtome)]</li><br />
</ul><br />
</li><br />
</ul><br />
</li><br />
<li><br />
Confocal microscopes<br />
<ul><br />
<li>[http://www.my.calendars.net/leica_lsm Leica LSM]</li><br />
</ul><br />
</li><br />
<li><br />
Cryostats<br />
<ul><br />
<li>[http://www.my.calendars.net/cryostat1 Cryostat 1]</li><br />
<li>[http://www.my.calendars.net/cryostat2 Cryostat 2]</li><br />
</ul><br />
</li><br />
<li><br />
Microtome<br />
<ul><br />
<li>[http://www.my.calendars.net/microtome Microtome]</li><br />
</ul><br />
</li><br />
<li><br />
Paraffin embedding station<br />
<ul><br />
<li>[http://www.my.calendars.net/wax_station Paraffin embedding station]</li><br />
</ul><br />
</li><br />
</ul><br />
<br />
== Genetics ==<br />
=== Transgenic lines ===<br />
<ul><br />
<li>[[Transgenic_axolotl_lines|Axolotl (A.mexicanum)]]</li><br />
<li>[[Transgenic_frog_lines|Frog (X.laevis)]]</li><br />
</ul><br />
<br />
=== Markers ===<br />
{| class="wikitable sortable"<br />
!style="width: 150px" | Marker<br />
!style="width: 250px" | Full name<br />
!style="width: 250px" | Target<br />
!style="width: 450px" | Remarks<br />
|-<br />
|DAPI/Hoechst<br />
|<br />
|Nuclei<br />
|Incorporates into the DNA<br />
|-<br />
|PCNA<br />
|Proliferating-Cell-Nuclear-Antigen<br />
|Dividing cells<br />
|<br />
|-<br />
|SOX2<br />
|<br />
|Preferentially neuronal lineage<br />
|Progenitor marker for both spinal cord and brain<br />
|-<br />
|PAX6<br />
|<br />
|Brain/spinal cord<br />
|<br />
|-<br />
|PAX7<br />
|<br />
|Satellite cells/spinal cord/brain<br />
|<br />
|-<br />
|MHC<br />
|Myosin heavy chain<br />
|Muscle fibers<br />
|<br />
|-<br />
|MYF5<br />
|<br />
|Muscle fibers<br />
|Labels cycling myoblasts<br />
|-<br />
|ßIII-tubulin<br />
|<br />
|Axons<br />
|<br />
|-<br />
|MBP<br />
|Myelin basic protein<br />
|Schwann cells<br />
|<br />
|-<br />
|PRRX1<br />
|<br />
|Blastema/mesodermal cells of limb bud<br />
|<br />
|-<br />
|SMA<br />
|<br />
|Blood vessels/endothelial cells<br />
|<br />
|-<br />
|GFAP<br />
|Glial fibrillary acidic protein<br />
|Glia<br />
|<br />
|-<br />
|NeuN<br />
|<br />
|Differentiated nerve<br />
|<br />
|-<br />
|LEU7<br />
|<br />
|Schwann cells<br />
|<br />
|-<br />
|XBRA<br />
|Xbrachyury<br />
|Mesoderm during gastrula stage<br />
|<br />
|-<br />
|MSX1<br />
|<br />
|Undifferentiated cells<br />
|Transcriptional repressor during embryogenesis<br />
|-<br />
|Trypan blue<br />
|<br />
|Dead tissues or cells<br />
|Vital stain<br />
|-<br />
|MEF2C<br />
|<br />
|Differentiated muscle cells<br />
|<br />
|-<br />
|PH3<br />
|<br />
|Mitotic cells<br />
|<br />
|-<br />
|BrdU<br />
|<br />
|Cells in S-phase<br />
|<br />
|-<br />
|CASP3<br />
|<br />
|Dying cells<br />
|<br />
|-<br />
|GDF5<br />
|<br />
|Joints<br />
|Joint development marker<br />
|-<br />
|Survivin<br />
|<br />
|Cleavage furrow<br />
|<br />
|-<br />
|MAP2<br />
|<br />
|<br />
|<br />
|-<br />
|SOX9<br />
|<br />
|Cartillage progenitors<br />
|<br />
|}<br />
<br />
== Digital data ==<br />
Over the years the members of the lab have produced a lot of different data: Sanger sequences, EST libraries, images and so on. <br />
Select a category from the list below in order to view or download the data.<br />
<br />
=== Fileservers ===<br />
{| class="wikitable"<br />
!style="width: 350px" | Location<br />
!style="width: 250px" | Volume size<br />
!style="width: 350px" | Description<br />
!style="width: 350px" | Access<br />
!style="width: 350px" | Location (console only)<br />
|-<br />
|//biodata/groups/<b>crtd_tanaka</b><br />
|16 TB<br />
|General purpose storage space<br />
|Entire Tanaka lab<br />
|<i>biocluster:</i> <b>/group/crtd_tanaka</b><br />
|-<br />
|//biodata/groups/<b>tanaka-ests</b><br />
|247 GB<br />
|EST sequences<br />
|Entire Tanaka lab<br />
|<i>biocluster:</i> <b>/group/tanaka-ests</b><br />
|-<br />
|//biodata/groups/<b>axolotl-transcriptome</b><br />
|500 GB<br />
|Axolotl transcriptome data<br />
|Elly, Sergej<br />
|<i>biocluster:</i> <b>/projects/axolotl-transcriptome</b><br />
|-<br />
|//biodata/groups/<b>tanaka-saori</b><br />
|878 GB<br />
|Special directory for Saori's data<br />
|Elly, Saori, Sergej<br />
|<i>biocluster:</i> <b>/group/tanaka-saori</b><br />
|}<br />
<br />
{{Tip|The path is different, when accessing the file server from the console.}}<br />
<br />
=== Literature ===<br />
<ul><br />
<li>[[Literature#Theses|Theses]]</li><br />
<li>[[Literature#Publications|Publications]]</li><br />
</ul><br />
<br />
=== Databases ===<br />
<ul><br />
<li>[http://est.age.mpg.de/axolotl/ Axolotl transcriptome] website contains the Axolotl transcriptome assemblies</li><br />
<li>[http://newtomics.mpi-bn.mpg.de/ Newt transcriptome] website contains the Newt transcriptome assembly</li><br />
<li>[http://sandberg.cmb.ki.se/redspottednewt/ Red spotted newt transcriptome] website contains the red spotted newt transcriptome assembly</li><br />
<li>[https://python-srv1.mpi-cbg.de/axolotl/cgi-bin/login.cgi Axolotl EST] database contains several ESTs and also some additional information, e.g. the position of the well with the corresponding insert in the Blastema (BL) or Neural tube (NT) library.</li><br />
<li>[http://est.age.mpg.de/ Axologle] database contains expression profiling data of Axolotl limb regeneration</li><br />
<li>[http://est.age.mpg.de/blast/blast.html Axolotl BLAST] database contains several different BLAST-able Axolotl transciptome assemblies</li><br />
</ul><br />
<br />
=== Datasets ===<br />
<ul><br />
<li>[[Datasets#Sequences|Sequences]]<br />
<ul><br />
<li>[[Datasets#Illumina|Illumina]]</li><br />
<li>[[Datasets#Sanger|Sanger]]</li><br />
<li>[[Datasets#Roche.2F454|Roche/454]]</li><br />
</ul><br />
</li><br />
<li>[[Datasets#Microarrays|Microarrays]]<br />
</ul><br />
<br />
=== Interesting links ===<br />
<ul><br />
<li>[http://www.nytimes.com/video/2013/02/27/science/100000002087758/finding-the-visible-in-the-invisible.html Visible in the invisible]: a movie introducing a new image processing ana analysis technique developed at the MIT.</li><br />
</ul><br />
<br />
== Lab life ==<br />
<ul><br />
<li>[[Lab_photos|Lab photos]]</li><br />
<li>Further pictures can be found in <b>/biodata/groups/crtd_tanaka/LabFun/</b></li><br />
<li>The recepies for Heino's farewell present can be found under <b>/biodata/groups/crtd_tanaka/LabFun/Heino's farewell present/</b></li><br />
<li>The video of the visit of the EU commissioner can be found under <b>/biodata/groups/crtd_tanaka/LabFun/</b></li><br />
</ul></div>
Serghein
https://wiki.tanakalab.org/index.php?title=Overview&diff=284
Overview
2013-07-16T13:33:35Z
<p>Serghein: /* Markers */</p>
<hr />
<div>== Introduction ==<br />
On the pages listed below you can find most common protocols used in the lab as well as a list of lab duties along with the names of the responsible persons. Please, contact the responsible persons if you have any question, suggestions or troubles.<br />
<br />
== Axolotl ==<br />
<br />
=== Maintainance ===<br />
In this section you will find some general information on how to [[Axolotl#Maintaining_the_axolotls|maintain]] the animals.<br />
<br />
=== Feeding ===<br />
This section will give you an overview of how to [[Axolotl#Feeding|feed]] the axolotls.<br />
<br />
=== Interesting observations ===<br />
In the following section you can find some [[Axolotl#Interesting_observations|interesting observations]] concerning the axolotl, its behavior, caveats of the transgenics and many more.<br />
<br />
== Lab duties ==<br />
<ul><br />
=== Chemicals ===<br />
<li>[[Antibiotics|Antibiotics]]</li><br />
<li>[[Benzocaine|Benzocaine]]</li><br />
<li>[[Fibronectin|Fibronectin]]</li><br />
<li>[[Gelatine|Gelatine]]</li><br />
<li>[[Liquid_nitrogen|Liquid nitrogen]]</li><br />
<li>[[Primary_antibodies|Primary antibodies]]</li><br />
<li>[[Secondary_antibodies|Secondary antibodies]]</li><br />
<li>[[Serum_immunostaining|Serum immunostaining]]</li><br />
<br />
=== Hardware ===<br />
<li>[[Autoclave|Autoclave]]</li><br />
<li>[[Cryostat|Cryostat]]</li><br />
<li>[[Dissecting_microscopes|Dissecting microscopes]]</li><br />
<li>[[Leica_confocal_microscope|Leica confocal microscope]]</li><br />
<li>[[Vacuum_pumps|Vacuum pumps]]</li><br />
<li>[[Waterbath|Waterbath]]</li><br />
<br />
=== General ===<br />
<li>[[Ordering_common_stuff|Ordering common stuff]]</li><br />
<li>[[Heat_shock_competent_cells|Heat-shock competent cells]]</li><br />
</ul><br />
<br />
<br />
== Protocols ==<br />
<ul><br />
=== Cell culture ===<br />
<li>[[Blastema_cells|Blastema cells]]</li><br />
<li>[[Baculovirus_titration|Baculovirus titration]]</li><br />
<li>[[Myoblasts_electroporation|Myoblasts electroporation]]</li><br />
<li>[[Adhesive_cell_culture|Adhesive cell culture]]</li><br />
<li>[[Electroporation_of_blastema_cells|Electroporation of blastema cells]]</li><br />
<li>[[Electroporation_of_nec|Electroporation of neural epithelia cells (axolotl spinal cord)]]</li><br />
<li>[[mESC_culture|mESC culture/Cyst formation]]</li><br />
<li>[[Neurosphere_culture|Neurosphere culture]]</li><br />
=== Histology ===<br />
<li>[[Double_Immunostaining_via_antigen_retrieval|Double Immunostaining via antigen retrieval (Sherry)]]</li><br />
=== Molecular biology ===<br />
<li>[[Metamorphosis_protocol|Metamorphosis protocol (Sherry)]]</li><br />
</ul><br />
<br />
== Booking calendars ==<br />
Since some pieces of hardware are used intensively it is necessary to book them in advance. The links to the corresponding booking calendars are listed below.<br />
<ul><br />
<li><br />
Fluorescence microscopes<br />
<ul><br />
<li>[http://www.my.calendars.net/olympusszx16 Olympus SZX 16]</li><br />
<li>[http://www.my.calendars.net/new_olympus/ New Olympus SZX 16]</li><br />
<li>[http://www.my.calendars.net/Olympus_OVK Olympus OVK]</li><br />
<li>[http://www.my.calendars.net/axio_observer/ Axio Observer]</li><br />
</ul><br />
</li><br />
<li><br />
Microinjectors and electroporators and dissecting microscope<br />
<ul><br />
<li>Room 0.232<br />
<ul> <br />
<li>[http://www.my.calendars.net/electroporator Nepa Gene]</li><br />
<li>[http://www.my.calendars.net/electroporator2 ECM 830]</li><br />
<li>[http://www.my.calendars.net/stereoscope2/d01/11/2012 Olympus dissecting microscope]</li><br />
</ul><br />
</li><br />
<li>Lab<br />
<ul><br />
<li>[http://www.my.calendars.net/OlympusLab Olympus (next to the axolotls)]</li><br />
<li>[http://www.my.calendars.net/OlympusLab2 Olympus (next to the Microtome)]</li><br />
</ul><br />
</li><br />
</ul><br />
</li><br />
<li><br />
Confocal microscopes<br />
<ul><br />
<li>[http://www.my.calendars.net/leica_lsm Leica LSM]</li><br />
</ul><br />
</li><br />
<li><br />
Cryostats<br />
<ul><br />
<li>[http://www.my.calendars.net/cryostat1 Cryostat 1]</li><br />
<li>[http://www.my.calendars.net/cryostat2 Cryostat 2]</li><br />
</ul><br />
</li><br />
<li><br />
Microtome<br />
<ul><br />
<li>[http://www.my.calendars.net/microtome Microtome]</li><br />
</ul><br />
</li><br />
<li><br />
Paraffin embedding station<br />
<ul><br />
<li>[http://www.my.calendars.net/wax_station Paraffin embedding station]</li><br />
</ul><br />
</li><br />
</ul><br />
<br />
== Genetics ==<br />
=== Transgenic lines ===<br />
<ul><br />
<li>[[Transgenic_axolotl_lines|Axolotl (A.mexicanum)]]</li><br />
<li>[[Transgenic_frog_lines|Frog (X.laevis)]]</li><br />
</ul><br />
<br />
=== Markers ===<br />
{| class="wikitable sortable"<br />
!style="width: 150px" | Marker<br />
!style="width: 250px" | Full name<br />
!style="width: 250px" | Target<br />
!style="width: 450px" | Remarks<br />
|-<br />
|DAPI/Hoechst<br />
|<br />
|Nuclei<br />
|Incorporates into the DNA<br />
|-<br />
|PCNA<br />
|Proliferating-Cell-Nuclear-Antigen<br />
|Dividing cells<br />
|<br />
|-<br />
|Sox2<br />
|<br />
|Preferentially neuronal lineage<br />
|Progenitor marker for both spinal cord and brain<br />
|-<br />
|PAX6<br />
|<br />
|Brain/spinal cord<br />
|<br />
|-<br />
|PAX7<br />
|<br />
|Satellite cells/spinal cord/brain<br />
|<br />
|-<br />
|MHC<br />
|Myosin heavy chain<br />
|Muscle fibers<br />
|<br />
|-<br />
|Myf5<br />
|<br />
|Muscle fibers<br />
|Labels cycling myoblasts<br />
|-<br />
|ßIII-tubulin<br />
|<br />
|Axons<br />
|<br />
|-<br />
|MBP<br />
|Myelin basic protein<br />
|Schwann cells<br />
|<br />
|-<br />
|Prrx1<br />
|<br />
|Blastema/mesodermal cells of limb bud<br />
|<br />
|-<br />
|SMA<br />
|<br />
|Blood vessels/endothelial cells<br />
|<br />
|-<br />
|GFAP<br />
|Glial fibrillary acidic protein<br />
|Glia<br />
|<br />
|-<br />
|NeuN<br />
|<br />
|Differentiated nerve<br />
|<br />
|-<br />
|Leu7<br />
|<br />
|Schwann cells<br />
|<br />
|-<br />
|Xbra<br />
|Xbrachyury<br />
|Mesoderm during gastrula stage<br />
|<br />
|-<br />
|Msx1<br />
|<br />
|Undifferentiated cells<br />
|Transcriptional repressor during embryogenesis<br />
|-<br />
|Trypan blue<br />
|<br />
|Dead tissues or cells<br />
|Vital stain<br />
|-<br />
|Mef2c<br />
|<br />
|Differentiated muscle cells<br />
|<br />
|-<br />
|PH3<br />
|<br />
|Mitotic cells<br />
|<br />
|-<br />
|BrdU<br />
|<br />
|Cells in S-phase<br />
|<br />
|-<br />
|Casp3<br />
|<br />
|Dying cells<br />
|<br />
|-<br />
|Gdf5<br />
|<br />
|Joints<br />
|Joint development marker<br />
|-<br />
|Survivin<br />
|<br />
|Cleavage furrow<br />
|<br />
|-<br />
|MAP2<br />
|<br />
|<br />
|<br />
|-<br />
|SOX9<br />
|<br />
|Cartillage progenitors<br />
|<br />
|}<br />
<br />
== Digital data ==<br />
Over the years the members of the lab have produced a lot of different data: Sanger sequences, EST libraries, images and so on. <br />
Select a category from the list below in order to view or download the data.<br />
<br />
=== Fileservers ===<br />
{| class="wikitable"<br />
!style="width: 350px" | Location<br />
!style="width: 250px" | Volume size<br />
!style="width: 350px" | Description<br />
!style="width: 350px" | Access<br />
!style="width: 350px" | Location (console only)<br />
|-<br />
|//biodata/groups/<b>crtd_tanaka</b><br />
|16 TB<br />
|General purpose storage space<br />
|Entire Tanaka lab<br />
|<i>biocluster:</i> <b>/group/crtd_tanaka</b><br />
|-<br />
|//biodata/groups/<b>tanaka-ests</b><br />
|247 GB<br />
|EST sequences<br />
|Entire Tanaka lab<br />
|<i>biocluster:</i> <b>/group/tanaka-ests</b><br />
|-<br />
|//biodata/groups/<b>axolotl-transcriptome</b><br />
|500 GB<br />
|Axolotl transcriptome data<br />
|Elly, Sergej<br />
|<i>biocluster:</i> <b>/projects/axolotl-transcriptome</b><br />
|-<br />
|//biodata/groups/<b>tanaka-saori</b><br />
|878 GB<br />
|Special directory for Saori's data<br />
|Elly, Saori, Sergej<br />
|<i>biocluster:</i> <b>/group/tanaka-saori</b><br />
|}<br />
<br />
{{Tip|The path is different, when accessing the file server from the console.}}<br />
<br />
=== Literature ===<br />
<ul><br />
<li>[[Literature#Theses|Theses]]</li><br />
<li>[[Literature#Publications|Publications]]</li><br />
</ul><br />
<br />
=== Databases ===<br />
<ul><br />
<li>[http://est.age.mpg.de/axolotl/ Axolotl transcriptome] website contains the Axolotl transcriptome assemblies</li><br />
<li>[http://newtomics.mpi-bn.mpg.de/ Newt transcriptome] website contains the Newt transcriptome assembly</li><br />
<li>[http://sandberg.cmb.ki.se/redspottednewt/ Red spotted newt transcriptome] website contains the red spotted newt transcriptome assembly</li><br />
<li>[https://python-srv1.mpi-cbg.de/axolotl/cgi-bin/login.cgi Axolotl EST] database contains several ESTs and also some additional information, e.g. the position of the well with the corresponding insert in the Blastema (BL) or Neural tube (NT) library.</li><br />
<li>[http://est.age.mpg.de/ Axologle] database contains expression profiling data of Axolotl limb regeneration</li><br />
<li>[http://est.age.mpg.de/blast/blast.html Axolotl BLAST] database contains several different BLAST-able Axolotl transciptome assemblies</li><br />
</ul><br />
<br />
=== Datasets ===<br />
<ul><br />
<li>[[Datasets#Sequences|Sequences]]<br />
<ul><br />
<li>[[Datasets#Illumina|Illumina]]</li><br />
<li>[[Datasets#Sanger|Sanger]]</li><br />
<li>[[Datasets#Roche.2F454|Roche/454]]</li><br />
</ul><br />
</li><br />
<li>[[Datasets#Microarrays|Microarrays]]<br />
</ul><br />
<br />
=== Interesting links ===<br />
<ul><br />
<li>[http://www.nytimes.com/video/2013/02/27/science/100000002087758/finding-the-visible-in-the-invisible.html Visible in the invisible]: a movie introducing a new image processing ana analysis technique developed at the MIT.</li><br />
</ul><br />
<br />
== Lab life ==<br />
<ul><br />
<li>[[Lab_photos|Lab photos]]</li><br />
<li>Further pictures can be found in <b>/biodata/groups/crtd_tanaka/LabFun/</b></li><br />
<li>The recepies for Heino's farewell present can be found under <b>/biodata/groups/crtd_tanaka/LabFun/Heino's farewell present/</b></li><br />
<li>The video of the visit of the EU commissioner can be found under <b>/biodata/groups/crtd_tanaka/LabFun/</b></li><br />
</ul></div>
Serghein
https://wiki.tanakalab.org/index.php?title=Overview&diff=283
Overview
2013-07-16T12:49:42Z
<p>Serghein: /* Markers */</p>
<hr />
<div>== Introduction ==<br />
On the pages listed below you can find most common protocols used in the lab as well as a list of lab duties along with the names of the responsible persons. Please, contact the responsible persons if you have any question, suggestions or troubles.<br />
<br />
== Axolotl ==<br />
<br />
=== Maintainance ===<br />
In this section you will find some general information on how to [[Axolotl#Maintaining_the_axolotls|maintain]] the animals.<br />
<br />
=== Feeding ===<br />
This section will give you an overview of how to [[Axolotl#Feeding|feed]] the axolotls.<br />
<br />
=== Interesting observations ===<br />
In the following section you can find some [[Axolotl#Interesting_observations|interesting observations]] concerning the axolotl, its behavior, caveats of the transgenics and many more.<br />
<br />
== Lab duties ==<br />
<ul><br />
=== Chemicals ===<br />
<li>[[Antibiotics|Antibiotics]]</li><br />
<li>[[Benzocaine|Benzocaine]]</li><br />
<li>[[Fibronectin|Fibronectin]]</li><br />
<li>[[Gelatine|Gelatine]]</li><br />
<li>[[Liquid_nitrogen|Liquid nitrogen]]</li><br />
<li>[[Primary_antibodies|Primary antibodies]]</li><br />
<li>[[Secondary_antibodies|Secondary antibodies]]</li><br />
<li>[[Serum_immunostaining|Serum immunostaining]]</li><br />
<br />
=== Hardware ===<br />
<li>[[Autoclave|Autoclave]]</li><br />
<li>[[Cryostat|Cryostat]]</li><br />
<li>[[Dissecting_microscopes|Dissecting microscopes]]</li><br />
<li>[[Leica_confocal_microscope|Leica confocal microscope]]</li><br />
<li>[[Vacuum_pumps|Vacuum pumps]]</li><br />
<li>[[Waterbath|Waterbath]]</li><br />
<br />
=== General ===<br />
<li>[[Ordering_common_stuff|Ordering common stuff]]</li><br />
<li>[[Heat_shock_competent_cells|Heat-shock competent cells]]</li><br />
</ul><br />
<br />
<br />
== Protocols ==<br />
<ul><br />
=== Cell culture ===<br />
<li>[[Blastema_cells|Blastema cells]]</li><br />
<li>[[Baculovirus_titration|Baculovirus titration]]</li><br />
<li>[[Myoblasts_electroporation|Myoblasts electroporation]]</li><br />
<li>[[Adhesive_cell_culture|Adhesive cell culture]]</li><br />
<li>[[Electroporation_of_blastema_cells|Electroporation of blastema cells]]</li><br />
<li>[[Electroporation_of_nec|Electroporation of neural epithelia cells (axolotl spinal cord)]]</li><br />
<li>[[mESC_culture|mESC culture/Cyst formation]]</li><br />
<li>[[Neurosphere_culture|Neurosphere culture]]</li><br />
=== Histology ===<br />
<li>[[Double_Immunostaining_via_antigen_retrieval|Double Immunostaining via antigen retrieval (Sherry)]]</li><br />
=== Molecular biology ===<br />
<li>[[Metamorphosis_protocol|Metamorphosis protocol (Sherry)]]</li><br />
</ul><br />
<br />
== Booking calendars ==<br />
Since some pieces of hardware are used intensively it is necessary to book them in advance. The links to the corresponding booking calendars are listed below.<br />
<ul><br />
<li><br />
Fluorescence microscopes<br />
<ul><br />
<li>[http://www.my.calendars.net/olympusszx16 Olympus SZX 16]</li><br />
<li>[http://www.my.calendars.net/new_olympus/ New Olympus SZX 16]</li><br />
<li>[http://www.my.calendars.net/Olympus_OVK Olympus OVK]</li><br />
<li>[http://www.my.calendars.net/axio_observer/ Axio Observer]</li><br />
</ul><br />
</li><br />
<li><br />
Microinjectors and electroporators and dissecting microscope<br />
<ul><br />
<li>Room 0.232<br />
<ul> <br />
<li>[http://www.my.calendars.net/electroporator Nepa Gene]</li><br />
<li>[http://www.my.calendars.net/electroporator2 ECM 830]</li><br />
<li>[http://www.my.calendars.net/stereoscope2/d01/11/2012 Olympus dissecting microscope]</li><br />
</ul><br />
</li><br />
<li>Lab<br />
<ul><br />
<li>[http://www.my.calendars.net/OlympusLab Olympus (next to the axolotls)]</li><br />
<li>[http://www.my.calendars.net/OlympusLab2 Olympus (next to the Microtome)]</li><br />
</ul><br />
</li><br />
</ul><br />
</li><br />
<li><br />
Confocal microscopes<br />
<ul><br />
<li>[http://www.my.calendars.net/leica_lsm Leica LSM]</li><br />
</ul><br />
</li><br />
<li><br />
Cryostats<br />
<ul><br />
<li>[http://www.my.calendars.net/cryostat1 Cryostat 1]</li><br />
<li>[http://www.my.calendars.net/cryostat2 Cryostat 2]</li><br />
</ul><br />
</li><br />
<li><br />
Microtome<br />
<ul><br />
<li>[http://www.my.calendars.net/microtome Microtome]</li><br />
</ul><br />
</li><br />
<li><br />
Paraffin embedding station<br />
<ul><br />
<li>[http://www.my.calendars.net/wax_station Paraffin embedding station]</li><br />
</ul><br />
</li><br />
</ul><br />
<br />
== Genetics ==<br />
=== Transgenic lines ===<br />
<ul><br />
<li>[[Transgenic_axolotl_lines|Axolotl (A.mexicanum)]]</li><br />
<li>[[Transgenic_frog_lines|Frog (X.laevis)]]</li><br />
</ul><br />
<br />
=== Markers ===<br />
{| class="wikitable sortable"<br />
!style="width: 150px" | Marker<br />
!style="width: 250px" | Full name<br />
!style="width: 250px" | Target<br />
!style="width: 450px" | Remarks<br />
|-<br />
|DAPI/Hoechst<br />
|<br />
|Nuclei<br />
|Incorporates into the DNA<br />
|-<br />
|PCNA<br />
|Proliferating-Cell-Nuclear-Antigen<br />
|Dividing cells<br />
|<br />
|-<br />
|Sox2<br />
|<br />
|Preferentially neuronal lineage<br />
|Progenitor marker for both spinal cord and brain<br />
|-<br />
|PAX6<br />
|<br />
|Brain/spinal cord<br />
|<br />
|-<br />
|PAX7<br />
|<br />
|Satellite cells/spinal cord/brain<br />
|<br />
|-<br />
|MHC<br />
|Myosin heavy chain<br />
|Muscle fibers<br />
|<br />
|-<br />
|Myf5<br />
|<br />
|Muscle fibers<br />
|Labels cycling myoblasts<br />
|-<br />
|ßIII-tubulin<br />
|<br />
|Axons<br />
|<br />
|-<br />
|MBP<br />
|Myelin basic protein<br />
|Schwann cells<br />
|<br />
|-<br />
|Prrx1<br />
|<br />
|Blastema/mesodermal cells of limb bud<br />
|<br />
|-<br />
|SMA<br />
|<br />
|Blood vessels/endothelial cells<br />
|<br />
|-<br />
|GFAP<br />
|Glial fibrillary acidic protein<br />
|Glia<br />
|<br />
|-<br />
|NeuN<br />
|<br />
|Differentiated nerve<br />
|<br />
|-<br />
|Leu7<br />
|<br />
|Schwann cells<br />
|<br />
|-<br />
|Xbra<br />
|Xbrachyury<br />
|Mesoderm during gastrula stage<br />
|<br />
|-<br />
|Msx1<br />
|<br />
|Undifferentiated cells<br />
|Transcriptional repressor during embryogenesis<br />
|-<br />
|Trypan blue<br />
|<br />
|Dead tissues or cells<br />
|Vital stain<br />
|-<br />
|Mef2c<br />
|<br />
|Differentiated muscle cells<br />
|<br />
|-<br />
|PH3<br />
|<br />
|Mitotic cells<br />
|<br />
|-<br />
|BrdU<br />
|<br />
|Cells in S-phase<br />
|<br />
|-<br />
|Casp3<br />
|<br />
|Dying cells<br />
|<br />
|-<br />
|Gdf5<br />
|<br />
|Joints<br />
|Joint development marker<br />
|-<br />
|Survivin<br />
|<br />
|Cleavage furrow<br />
|<br />
|}<br />
<br />
== Digital data ==<br />
Over the years the members of the lab have produced a lot of different data: Sanger sequences, EST libraries, images and so on. <br />
Select a category from the list below in order to view or download the data.<br />
<br />
=== Fileservers ===<br />
{| class="wikitable"<br />
!style="width: 350px" | Location<br />
!style="width: 250px" | Volume size<br />
!style="width: 350px" | Description<br />
!style="width: 350px" | Access<br />
!style="width: 350px" | Location (console only)<br />
|-<br />
|//biodata/groups/<b>crtd_tanaka</b><br />
|16 TB<br />
|General purpose storage space<br />
|Entire Tanaka lab<br />
|<i>biocluster:</i> <b>/group/crtd_tanaka</b><br />
|-<br />
|//biodata/groups/<b>tanaka-ests</b><br />
|247 GB<br />
|EST sequences<br />
|Entire Tanaka lab<br />
|<i>biocluster:</i> <b>/group/tanaka-ests</b><br />
|-<br />
|//biodata/groups/<b>axolotl-transcriptome</b><br />
|500 GB<br />
|Axolotl transcriptome data<br />
|Elly, Sergej<br />
|<i>biocluster:</i> <b>/projects/axolotl-transcriptome</b><br />
|-<br />
|//biodata/groups/<b>tanaka-saori</b><br />
|878 GB<br />
|Special directory for Saori's data<br />
|Elly, Saori, Sergej<br />
|<i>biocluster:</i> <b>/group/tanaka-saori</b><br />
|}<br />
<br />
{{Tip|The path is different, when accessing the file server from the console.}}<br />
<br />
=== Literature ===<br />
<ul><br />
<li>[[Literature#Theses|Theses]]</li><br />
<li>[[Literature#Publications|Publications]]</li><br />
</ul><br />
<br />
=== Databases ===<br />
<ul><br />
<li>[http://est.age.mpg.de/axolotl/ Axolotl transcriptome] website contains the Axolotl transcriptome assemblies</li><br />
<li>[http://newtomics.mpi-bn.mpg.de/ Newt transcriptome] website contains the Newt transcriptome assembly</li><br />
<li>[http://sandberg.cmb.ki.se/redspottednewt/ Red spotted newt transcriptome] website contains the red spotted newt transcriptome assembly</li><br />
<li>[https://python-srv1.mpi-cbg.de/axolotl/cgi-bin/login.cgi Axolotl EST] database contains several ESTs and also some additional information, e.g. the position of the well with the corresponding insert in the Blastema (BL) or Neural tube (NT) library.</li><br />
<li>[http://est.age.mpg.de/ Axologle] database contains expression profiling data of Axolotl limb regeneration</li><br />
<li>[http://est.age.mpg.de/blast/blast.html Axolotl BLAST] database contains several different BLAST-able Axolotl transciptome assemblies</li><br />
</ul><br />
<br />
=== Datasets ===<br />
<ul><br />
<li>[[Datasets#Sequences|Sequences]]<br />
<ul><br />
<li>[[Datasets#Illumina|Illumina]]</li><br />
<li>[[Datasets#Sanger|Sanger]]</li><br />
<li>[[Datasets#Roche.2F454|Roche/454]]</li><br />
</ul><br />
</li><br />
<li>[[Datasets#Microarrays|Microarrays]]<br />
</ul><br />
<br />
=== Interesting links ===<br />
<ul><br />
<li>[http://www.nytimes.com/video/2013/02/27/science/100000002087758/finding-the-visible-in-the-invisible.html Visible in the invisible]: a movie introducing a new image processing ana analysis technique developed at the MIT.</li><br />
</ul><br />
<br />
== Lab life ==<br />
<ul><br />
<li>[[Lab_photos|Lab photos]]</li><br />
<li>Further pictures can be found in <b>/biodata/groups/crtd_tanaka/LabFun/</b></li><br />
<li>The recepies for Heino's farewell present can be found under <b>/biodata/groups/crtd_tanaka/LabFun/Heino's farewell present/</b></li><br />
<li>The video of the visit of the EU commissioner can be found under <b>/biodata/groups/crtd_tanaka/LabFun/</b></li><br />
</ul></div>
Serghein
https://wiki.tanakalab.org/index.php?title=Overview&diff=282
Overview
2013-07-16T12:49:16Z
<p>Serghein: /* Markers */</p>
<hr />
<div>== Introduction ==<br />
On the pages listed below you can find most common protocols used in the lab as well as a list of lab duties along with the names of the responsible persons. Please, contact the responsible persons if you have any question, suggestions or troubles.<br />
<br />
== Axolotl ==<br />
<br />
=== Maintainance ===<br />
In this section you will find some general information on how to [[Axolotl#Maintaining_the_axolotls|maintain]] the animals.<br />
<br />
=== Feeding ===<br />
This section will give you an overview of how to [[Axolotl#Feeding|feed]] the axolotls.<br />
<br />
=== Interesting observations ===<br />
In the following section you can find some [[Axolotl#Interesting_observations|interesting observations]] concerning the axolotl, its behavior, caveats of the transgenics and many more.<br />
<br />
== Lab duties ==<br />
<ul><br />
=== Chemicals ===<br />
<li>[[Antibiotics|Antibiotics]]</li><br />
<li>[[Benzocaine|Benzocaine]]</li><br />
<li>[[Fibronectin|Fibronectin]]</li><br />
<li>[[Gelatine|Gelatine]]</li><br />
<li>[[Liquid_nitrogen|Liquid nitrogen]]</li><br />
<li>[[Primary_antibodies|Primary antibodies]]</li><br />
<li>[[Secondary_antibodies|Secondary antibodies]]</li><br />
<li>[[Serum_immunostaining|Serum immunostaining]]</li><br />
<br />
=== Hardware ===<br />
<li>[[Autoclave|Autoclave]]</li><br />
<li>[[Cryostat|Cryostat]]</li><br />
<li>[[Dissecting_microscopes|Dissecting microscopes]]</li><br />
<li>[[Leica_confocal_microscope|Leica confocal microscope]]</li><br />
<li>[[Vacuum_pumps|Vacuum pumps]]</li><br />
<li>[[Waterbath|Waterbath]]</li><br />
<br />
=== General ===<br />
<li>[[Ordering_common_stuff|Ordering common stuff]]</li><br />
<li>[[Heat_shock_competent_cells|Heat-shock competent cells]]</li><br />
</ul><br />
<br />
<br />
== Protocols ==<br />
<ul><br />
=== Cell culture ===<br />
<li>[[Blastema_cells|Blastema cells]]</li><br />
<li>[[Baculovirus_titration|Baculovirus titration]]</li><br />
<li>[[Myoblasts_electroporation|Myoblasts electroporation]]</li><br />
<li>[[Adhesive_cell_culture|Adhesive cell culture]]</li><br />
<li>[[Electroporation_of_blastema_cells|Electroporation of blastema cells]]</li><br />
<li>[[Electroporation_of_nec|Electroporation of neural epithelia cells (axolotl spinal cord)]]</li><br />
<li>[[mESC_culture|mESC culture/Cyst formation]]</li><br />
<li>[[Neurosphere_culture|Neurosphere culture]]</li><br />
=== Histology ===<br />
<li>[[Double_Immunostaining_via_antigen_retrieval|Double Immunostaining via antigen retrieval (Sherry)]]</li><br />
=== Molecular biology ===<br />
<li>[[Metamorphosis_protocol|Metamorphosis protocol (Sherry)]]</li><br />
</ul><br />
<br />
== Booking calendars ==<br />
Since some pieces of hardware are used intensively it is necessary to book them in advance. The links to the corresponding booking calendars are listed below.<br />
<ul><br />
<li><br />
Fluorescence microscopes<br />
<ul><br />
<li>[http://www.my.calendars.net/olympusszx16 Olympus SZX 16]</li><br />
<li>[http://www.my.calendars.net/new_olympus/ New Olympus SZX 16]</li><br />
<li>[http://www.my.calendars.net/Olympus_OVK Olympus OVK]</li><br />
<li>[http://www.my.calendars.net/axio_observer/ Axio Observer]</li><br />
</ul><br />
</li><br />
<li><br />
Microinjectors and electroporators and dissecting microscope<br />
<ul><br />
<li>Room 0.232<br />
<ul> <br />
<li>[http://www.my.calendars.net/electroporator Nepa Gene]</li><br />
<li>[http://www.my.calendars.net/electroporator2 ECM 830]</li><br />
<li>[http://www.my.calendars.net/stereoscope2/d01/11/2012 Olympus dissecting microscope]</li><br />
</ul><br />
</li><br />
<li>Lab<br />
<ul><br />
<li>[http://www.my.calendars.net/OlympusLab Olympus (next to the axolotls)]</li><br />
<li>[http://www.my.calendars.net/OlympusLab2 Olympus (next to the Microtome)]</li><br />
</ul><br />
</li><br />
</ul><br />
</li><br />
<li><br />
Confocal microscopes<br />
<ul><br />
<li>[http://www.my.calendars.net/leica_lsm Leica LSM]</li><br />
</ul><br />
</li><br />
<li><br />
Cryostats<br />
<ul><br />
<li>[http://www.my.calendars.net/cryostat1 Cryostat 1]</li><br />
<li>[http://www.my.calendars.net/cryostat2 Cryostat 2]</li><br />
</ul><br />
</li><br />
<li><br />
Microtome<br />
<ul><br />
<li>[http://www.my.calendars.net/microtome Microtome]</li><br />
</ul><br />
</li><br />
<li><br />
Paraffin embedding station<br />
<ul><br />
<li>[http://www.my.calendars.net/wax_station Paraffin embedding station]</li><br />
</ul><br />
</li><br />
</ul><br />
<br />
== Genetics ==<br />
=== Transgenic lines ===<br />
<ul><br />
<li>[[Transgenic_axolotl_lines|Axolotl (A.mexicanum)]]</li><br />
<li>[[Transgenic_frog_lines|Frog (X.laevis)]]</li><br />
</ul><br />
<br />
=== Markers ===<br />
{| class="wikitable sortable"<br />
!style="width: 150px" | Marker<br />
!style="width: 250px" | Full name<br />
!style="width: 250px" | Target<br />
!style="width: 450px" | Remarks<br />
|-<br />
|DAPI/Hoechst<br />
|<br />
|Nuclei<br />
|Incorporates into the DNA<br />
|-<br />
|PCNA<br />
|Proliferating-Cell-Nuclear-Antigen<br />
|Dividing cells<br />
|<br />
|-<br />
|Sox2<br />
|<br />
|Preferentially neuronal lineage<br />
|Progenitor marker for both spinal cord and brain<br />
|-<br />
|PAX6<br />
|<br />
|Brain / spinal cord<br />
|<br />
|-<br />
|PAX7<br />
|<br />
|Satellite cells / spinal cord / brain<br />
|<br />
|-<br />
|MHC<br />
|Myosin heavy chain<br />
|Muscle fibers<br />
|<br />
|-<br />
|Myf5<br />
|<br />
|Muscle fibers<br />
|Labels cycling myoblasts<br />
|-<br />
|ßIII-tubulin<br />
|<br />
|Axons<br />
|<br />
|-<br />
|MBP<br />
|Myelin basic protein<br />
|Schwann cells<br />
|<br />
|-<br />
|Prrx1<br />
|<br />
|Blastema/mesodermal cells of limb bud<br />
|<br />
|-<br />
|SMA<br />
|<br />
|Blood vessels/endothelial cells<br />
|<br />
|-<br />
|GFAP<br />
|Glial fibrillary acidic protein<br />
|Glia<br />
|<br />
|-<br />
|NeuN<br />
|<br />
|Differentiated nerve<br />
|<br />
|-<br />
|Leu7<br />
|<br />
|Schwann cells<br />
|<br />
|-<br />
|Xbra<br />
|Xbrachyury<br />
|Mesoderm during gastrula stage<br />
|<br />
|-<br />
|Msx1<br />
|<br />
|Undifferentiated cells<br />
|Transcriptional repressor during embryogenesis<br />
|-<br />
|Trypan blue<br />
|<br />
|Dead tissues or cells<br />
|Vital stain<br />
|-<br />
|Mef2c<br />
|<br />
|Differentiated muscle cells<br />
|<br />
|-<br />
|PH3<br />
|<br />
|Mitotic cells<br />
|<br />
|-<br />
|BrdU<br />
|<br />
|Cells in S-phase<br />
|<br />
|-<br />
|Casp3<br />
|<br />
|Dying cells<br />
|<br />
|-<br />
|Gdf5<br />
|<br />
|Joints<br />
|Joint development marker<br />
|-<br />
|Survivin<br />
|<br />
|Cleavage furrow<br />
|<br />
|}<br />
<br />
== Digital data ==<br />
Over the years the members of the lab have produced a lot of different data: Sanger sequences, EST libraries, images and so on. <br />
Select a category from the list below in order to view or download the data.<br />
<br />
=== Fileservers ===<br />
{| class="wikitable"<br />
!style="width: 350px" | Location<br />
!style="width: 250px" | Volume size<br />
!style="width: 350px" | Description<br />
!style="width: 350px" | Access<br />
!style="width: 350px" | Location (console only)<br />
|-<br />
|//biodata/groups/<b>crtd_tanaka</b><br />
|16 TB<br />
|General purpose storage space<br />
|Entire Tanaka lab<br />
|<i>biocluster:</i> <b>/group/crtd_tanaka</b><br />
|-<br />
|//biodata/groups/<b>tanaka-ests</b><br />
|247 GB<br />
|EST sequences<br />
|Entire Tanaka lab<br />
|<i>biocluster:</i> <b>/group/tanaka-ests</b><br />
|-<br />
|//biodata/groups/<b>axolotl-transcriptome</b><br />
|500 GB<br />
|Axolotl transcriptome data<br />
|Elly, Sergej<br />
|<i>biocluster:</i> <b>/projects/axolotl-transcriptome</b><br />
|-<br />
|//biodata/groups/<b>tanaka-saori</b><br />
|878 GB<br />
|Special directory for Saori's data<br />
|Elly, Saori, Sergej<br />
|<i>biocluster:</i> <b>/group/tanaka-saori</b><br />
|}<br />
<br />
{{Tip|The path is different, when accessing the file server from the console.}}<br />
<br />
=== Literature ===<br />
<ul><br />
<li>[[Literature#Theses|Theses]]</li><br />
<li>[[Literature#Publications|Publications]]</li><br />
</ul><br />
<br />
=== Databases ===<br />
<ul><br />
<li>[http://est.age.mpg.de/axolotl/ Axolotl transcriptome] website contains the Axolotl transcriptome assemblies</li><br />
<li>[http://newtomics.mpi-bn.mpg.de/ Newt transcriptome] website contains the Newt transcriptome assembly</li><br />
<li>[http://sandberg.cmb.ki.se/redspottednewt/ Red spotted newt transcriptome] website contains the red spotted newt transcriptome assembly</li><br />
<li>[https://python-srv1.mpi-cbg.de/axolotl/cgi-bin/login.cgi Axolotl EST] database contains several ESTs and also some additional information, e.g. the position of the well with the corresponding insert in the Blastema (BL) or Neural tube (NT) library.</li><br />
<li>[http://est.age.mpg.de/ Axologle] database contains expression profiling data of Axolotl limb regeneration</li><br />
<li>[http://est.age.mpg.de/blast/blast.html Axolotl BLAST] database contains several different BLAST-able Axolotl transciptome assemblies</li><br />
</ul><br />
<br />
=== Datasets ===<br />
<ul><br />
<li>[[Datasets#Sequences|Sequences]]<br />
<ul><br />
<li>[[Datasets#Illumina|Illumina]]</li><br />
<li>[[Datasets#Sanger|Sanger]]</li><br />
<li>[[Datasets#Roche.2F454|Roche/454]]</li><br />
</ul><br />
</li><br />
<li>[[Datasets#Microarrays|Microarrays]]<br />
</ul><br />
<br />
=== Interesting links ===<br />
<ul><br />
<li>[http://www.nytimes.com/video/2013/02/27/science/100000002087758/finding-the-visible-in-the-invisible.html Visible in the invisible]: a movie introducing a new image processing ana analysis technique developed at the MIT.</li><br />
</ul><br />
<br />
== Lab life ==<br />
<ul><br />
<li>[[Lab_photos|Lab photos]]</li><br />
<li>Further pictures can be found in <b>/biodata/groups/crtd_tanaka/LabFun/</b></li><br />
<li>The recepies for Heino's farewell present can be found under <b>/biodata/groups/crtd_tanaka/LabFun/Heino's farewell present/</b></li><br />
<li>The video of the visit of the EU commissioner can be found under <b>/biodata/groups/crtd_tanaka/LabFun/</b></li><br />
</ul></div>
Serghein
https://wiki.tanakalab.org/index.php?title=Overview&diff=281
Overview
2013-07-16T12:48:40Z
<p>Serghein: /* Markers */</p>
<hr />
<div>== Introduction ==<br />
On the pages listed below you can find most common protocols used in the lab as well as a list of lab duties along with the names of the responsible persons. Please, contact the responsible persons if you have any question, suggestions or troubles.<br />
<br />
== Axolotl ==<br />
<br />
=== Maintainance ===<br />
In this section you will find some general information on how to [[Axolotl#Maintaining_the_axolotls|maintain]] the animals.<br />
<br />
=== Feeding ===<br />
This section will give you an overview of how to [[Axolotl#Feeding|feed]] the axolotls.<br />
<br />
=== Interesting observations ===<br />
In the following section you can find some [[Axolotl#Interesting_observations|interesting observations]] concerning the axolotl, its behavior, caveats of the transgenics and many more.<br />
<br />
== Lab duties ==<br />
<ul><br />
=== Chemicals ===<br />
<li>[[Antibiotics|Antibiotics]]</li><br />
<li>[[Benzocaine|Benzocaine]]</li><br />
<li>[[Fibronectin|Fibronectin]]</li><br />
<li>[[Gelatine|Gelatine]]</li><br />
<li>[[Liquid_nitrogen|Liquid nitrogen]]</li><br />
<li>[[Primary_antibodies|Primary antibodies]]</li><br />
<li>[[Secondary_antibodies|Secondary antibodies]]</li><br />
<li>[[Serum_immunostaining|Serum immunostaining]]</li><br />
<br />
=== Hardware ===<br />
<li>[[Autoclave|Autoclave]]</li><br />
<li>[[Cryostat|Cryostat]]</li><br />
<li>[[Dissecting_microscopes|Dissecting microscopes]]</li><br />
<li>[[Leica_confocal_microscope|Leica confocal microscope]]</li><br />
<li>[[Vacuum_pumps|Vacuum pumps]]</li><br />
<li>[[Waterbath|Waterbath]]</li><br />
<br />
=== General ===<br />
<li>[[Ordering_common_stuff|Ordering common stuff]]</li><br />
<li>[[Heat_shock_competent_cells|Heat-shock competent cells]]</li><br />
</ul><br />
<br />
<br />
== Protocols ==<br />
<ul><br />
=== Cell culture ===<br />
<li>[[Blastema_cells|Blastema cells]]</li><br />
<li>[[Baculovirus_titration|Baculovirus titration]]</li><br />
<li>[[Myoblasts_electroporation|Myoblasts electroporation]]</li><br />
<li>[[Adhesive_cell_culture|Adhesive cell culture]]</li><br />
<li>[[Electroporation_of_blastema_cells|Electroporation of blastema cells]]</li><br />
<li>[[Electroporation_of_nec|Electroporation of neural epithelia cells (axolotl spinal cord)]]</li><br />
<li>[[mESC_culture|mESC culture/Cyst formation]]</li><br />
<li>[[Neurosphere_culture|Neurosphere culture]]</li><br />
=== Histology ===<br />
<li>[[Double_Immunostaining_via_antigen_retrieval|Double Immunostaining via antigen retrieval (Sherry)]]</li><br />
=== Molecular biology ===<br />
<li>[[Metamorphosis_protocol|Metamorphosis protocol (Sherry)]]</li><br />
</ul><br />
<br />
== Booking calendars ==<br />
Since some pieces of hardware are used intensively it is necessary to book them in advance. The links to the corresponding booking calendars are listed below.<br />
<ul><br />
<li><br />
Fluorescence microscopes<br />
<ul><br />
<li>[http://www.my.calendars.net/olympusszx16 Olympus SZX 16]</li><br />
<li>[http://www.my.calendars.net/new_olympus/ New Olympus SZX 16]</li><br />
<li>[http://www.my.calendars.net/Olympus_OVK Olympus OVK]</li><br />
<li>[http://www.my.calendars.net/axio_observer/ Axio Observer]</li><br />
</ul><br />
</li><br />
<li><br />
Microinjectors and electroporators and dissecting microscope<br />
<ul><br />
<li>Room 0.232<br />
<ul> <br />
<li>[http://www.my.calendars.net/electroporator Nepa Gene]</li><br />
<li>[http://www.my.calendars.net/electroporator2 ECM 830]</li><br />
<li>[http://www.my.calendars.net/stereoscope2/d01/11/2012 Olympus dissecting microscope]</li><br />
</ul><br />
</li><br />
<li>Lab<br />
<ul><br />
<li>[http://www.my.calendars.net/OlympusLab Olympus (next to the axolotls)]</li><br />
<li>[http://www.my.calendars.net/OlympusLab2 Olympus (next to the Microtome)]</li><br />
</ul><br />
</li><br />
</ul><br />
</li><br />
<li><br />
Confocal microscopes<br />
<ul><br />
<li>[http://www.my.calendars.net/leica_lsm Leica LSM]</li><br />
</ul><br />
</li><br />
<li><br />
Cryostats<br />
<ul><br />
<li>[http://www.my.calendars.net/cryostat1 Cryostat 1]</li><br />
<li>[http://www.my.calendars.net/cryostat2 Cryostat 2]</li><br />
</ul><br />
</li><br />
<li><br />
Microtome<br />
<ul><br />
<li>[http://www.my.calendars.net/microtome Microtome]</li><br />
</ul><br />
</li><br />
<li><br />
Paraffin embedding station<br />
<ul><br />
<li>[http://www.my.calendars.net/wax_station Paraffin embedding station]</li><br />
</ul><br />
</li><br />
</ul><br />
<br />
== Genetics ==<br />
=== Transgenic lines ===<br />
<ul><br />
<li>[[Transgenic_axolotl_lines|Axolotl (A.mexicanum)]]</li><br />
<li>[[Transgenic_frog_lines|Frog (X.laevis)]]</li><br />
</ul><br />
<br />
=== Markers ===<br />
{| class="wikitable sortable"<br />
!style="width: 150px" | Marker<br />
!style="width: 250px" | Full name<br />
!style="width: 250px" | Target<br />
!style="width: 450px" | Remarks<br />
|-<br />
|DAPI/Hoechst<br />
|<br />
|Nuclei<br />
|Incorporates into the DNA<br />
|-<br />
|PCNA<br />
|Proliferating-Cell-Nuclear-Antigen<br />
|Dividing cells<br />
|<br />
|-<br />
|Sox2<br />
|<br />
|Preferentially neuronal lineage<br />
|Progenitor marker for both spinal cord and brain<br />
|-<br />
|PAX6<br />
|<br />
|Brain/spinal Cord<br />
|<br />
|-<br />
|PAX7<br />
|<br />
|Satellite cells/spinal Cord/brain<br />
|<br />
|-<br />
|MHC<br />
|Myosin heavy chain<br />
|Muscle fibers<br />
|<br />
|-<br />
|Myf5<br />
|<br />
|Muscle fibers<br />
|Labels cycling myoblasts<br />
|-<br />
|ßIII-tubulin<br />
|<br />
|Axons<br />
|<br />
|-<br />
|MBP<br />
|Myelin basic protein<br />
|Schwann cells<br />
|<br />
|-<br />
|Prrx1<br />
|<br />
|Blastema/mesodermal cells of limb bud<br />
|<br />
|-<br />
|SMA<br />
|<br />
|Blood vessels/endothelial cells<br />
|<br />
|-<br />
|GFAP<br />
|Glial fibrillary acidic protein<br />
|Glia<br />
|<br />
|-<br />
|NeuN<br />
|<br />
|Differentiated nerve<br />
|<br />
|-<br />
|Leu7<br />
|<br />
|Schwann cells<br />
|<br />
|-<br />
|Xbra<br />
|Xbrachyury<br />
|Mesoderm during gastrula stage<br />
|<br />
|-<br />
|Msx1<br />
|<br />
|Undifferentiated cells<br />
|Transcriptional repressor during embryogenesis<br />
|-<br />
|Trypan blue<br />
|<br />
|Dead tissues or cells<br />
|Vital stain<br />
|-<br />
|Mef2c<br />
|<br />
|Differentiated muscle cells<br />
|<br />
|-<br />
|PH3<br />
|<br />
|Mitotic cells<br />
|<br />
|-<br />
|BrdU<br />
|<br />
|Cells in S-phase<br />
|<br />
|-<br />
|Casp3<br />
|<br />
|Dying cells<br />
|<br />
|-<br />
|Gdf5<br />
|<br />
|Joints<br />
|Joint development marker<br />
|-<br />
|Survivin<br />
|<br />
|Cleavage furrow<br />
|<br />
|}<br />
<br />
== Digital data ==<br />
Over the years the members of the lab have produced a lot of different data: Sanger sequences, EST libraries, images and so on. <br />
Select a category from the list below in order to view or download the data.<br />
<br />
=== Fileservers ===<br />
{| class="wikitable"<br />
!style="width: 350px" | Location<br />
!style="width: 250px" | Volume size<br />
!style="width: 350px" | Description<br />
!style="width: 350px" | Access<br />
!style="width: 350px" | Location (console only)<br />
|-<br />
|//biodata/groups/<b>crtd_tanaka</b><br />
|16 TB<br />
|General purpose storage space<br />
|Entire Tanaka lab<br />
|<i>biocluster:</i> <b>/group/crtd_tanaka</b><br />
|-<br />
|//biodata/groups/<b>tanaka-ests</b><br />
|247 GB<br />
|EST sequences<br />
|Entire Tanaka lab<br />
|<i>biocluster:</i> <b>/group/tanaka-ests</b><br />
|-<br />
|//biodata/groups/<b>axolotl-transcriptome</b><br />
|500 GB<br />
|Axolotl transcriptome data<br />
|Elly, Sergej<br />
|<i>biocluster:</i> <b>/projects/axolotl-transcriptome</b><br />
|-<br />
|//biodata/groups/<b>tanaka-saori</b><br />
|878 GB<br />
|Special directory for Saori's data<br />
|Elly, Saori, Sergej<br />
|<i>biocluster:</i> <b>/group/tanaka-saori</b><br />
|}<br />
<br />
{{Tip|The path is different, when accessing the file server from the console.}}<br />
<br />
=== Literature ===<br />
<ul><br />
<li>[[Literature#Theses|Theses]]</li><br />
<li>[[Literature#Publications|Publications]]</li><br />
</ul><br />
<br />
=== Databases ===<br />
<ul><br />
<li>[http://est.age.mpg.de/axolotl/ Axolotl transcriptome] website contains the Axolotl transcriptome assemblies</li><br />
<li>[http://newtomics.mpi-bn.mpg.de/ Newt transcriptome] website contains the Newt transcriptome assembly</li><br />
<li>[http://sandberg.cmb.ki.se/redspottednewt/ Red spotted newt transcriptome] website contains the red spotted newt transcriptome assembly</li><br />
<li>[https://python-srv1.mpi-cbg.de/axolotl/cgi-bin/login.cgi Axolotl EST] database contains several ESTs and also some additional information, e.g. the position of the well with the corresponding insert in the Blastema (BL) or Neural tube (NT) library.</li><br />
<li>[http://est.age.mpg.de/ Axologle] database contains expression profiling data of Axolotl limb regeneration</li><br />
<li>[http://est.age.mpg.de/blast/blast.html Axolotl BLAST] database contains several different BLAST-able Axolotl transciptome assemblies</li><br />
</ul><br />
<br />
=== Datasets ===<br />
<ul><br />
<li>[[Datasets#Sequences|Sequences]]<br />
<ul><br />
<li>[[Datasets#Illumina|Illumina]]</li><br />
<li>[[Datasets#Sanger|Sanger]]</li><br />
<li>[[Datasets#Roche.2F454|Roche/454]]</li><br />
</ul><br />
</li><br />
<li>[[Datasets#Microarrays|Microarrays]]<br />
</ul><br />
<br />
=== Interesting links ===<br />
<ul><br />
<li>[http://www.nytimes.com/video/2013/02/27/science/100000002087758/finding-the-visible-in-the-invisible.html Visible in the invisible]: a movie introducing a new image processing ana analysis technique developed at the MIT.</li><br />
</ul><br />
<br />
== Lab life ==<br />
<ul><br />
<li>[[Lab_photos|Lab photos]]</li><br />
<li>Further pictures can be found in <b>/biodata/groups/crtd_tanaka/LabFun/</b></li><br />
<li>The recepies for Heino's farewell present can be found under <b>/biodata/groups/crtd_tanaka/LabFun/Heino's farewell present/</b></li><br />
<li>The video of the visit of the EU commissioner can be found under <b>/biodata/groups/crtd_tanaka/LabFun/</b></li><br />
</ul></div>
Serghein
https://wiki.tanakalab.org/index.php?title=Overview&diff=280
Overview
2013-07-16T12:47:45Z
<p>Serghein: /* Markers */</p>
<hr />
<div>== Introduction ==<br />
On the pages listed below you can find most common protocols used in the lab as well as a list of lab duties along with the names of the responsible persons. Please, contact the responsible persons if you have any question, suggestions or troubles.<br />
<br />
== Axolotl ==<br />
<br />
=== Maintainance ===<br />
In this section you will find some general information on how to [[Axolotl#Maintaining_the_axolotls|maintain]] the animals.<br />
<br />
=== Feeding ===<br />
This section will give you an overview of how to [[Axolotl#Feeding|feed]] the axolotls.<br />
<br />
=== Interesting observations ===<br />
In the following section you can find some [[Axolotl#Interesting_observations|interesting observations]] concerning the axolotl, its behavior, caveats of the transgenics and many more.<br />
<br />
== Lab duties ==<br />
<ul><br />
=== Chemicals ===<br />
<li>[[Antibiotics|Antibiotics]]</li><br />
<li>[[Benzocaine|Benzocaine]]</li><br />
<li>[[Fibronectin|Fibronectin]]</li><br />
<li>[[Gelatine|Gelatine]]</li><br />
<li>[[Liquid_nitrogen|Liquid nitrogen]]</li><br />
<li>[[Primary_antibodies|Primary antibodies]]</li><br />
<li>[[Secondary_antibodies|Secondary antibodies]]</li><br />
<li>[[Serum_immunostaining|Serum immunostaining]]</li><br />
<br />
=== Hardware ===<br />
<li>[[Autoclave|Autoclave]]</li><br />
<li>[[Cryostat|Cryostat]]</li><br />
<li>[[Dissecting_microscopes|Dissecting microscopes]]</li><br />
<li>[[Leica_confocal_microscope|Leica confocal microscope]]</li><br />
<li>[[Vacuum_pumps|Vacuum pumps]]</li><br />
<li>[[Waterbath|Waterbath]]</li><br />
<br />
=== General ===<br />
<li>[[Ordering_common_stuff|Ordering common stuff]]</li><br />
<li>[[Heat_shock_competent_cells|Heat-shock competent cells]]</li><br />
</ul><br />
<br />
<br />
== Protocols ==<br />
<ul><br />
=== Cell culture ===<br />
<li>[[Blastema_cells|Blastema cells]]</li><br />
<li>[[Baculovirus_titration|Baculovirus titration]]</li><br />
<li>[[Myoblasts_electroporation|Myoblasts electroporation]]</li><br />
<li>[[Adhesive_cell_culture|Adhesive cell culture]]</li><br />
<li>[[Electroporation_of_blastema_cells|Electroporation of blastema cells]]</li><br />
<li>[[Electroporation_of_nec|Electroporation of neural epithelia cells (axolotl spinal cord)]]</li><br />
<li>[[mESC_culture|mESC culture/Cyst formation]]</li><br />
<li>[[Neurosphere_culture|Neurosphere culture]]</li><br />
=== Histology ===<br />
<li>[[Double_Immunostaining_via_antigen_retrieval|Double Immunostaining via antigen retrieval (Sherry)]]</li><br />
=== Molecular biology ===<br />
<li>[[Metamorphosis_protocol|Metamorphosis protocol (Sherry)]]</li><br />
</ul><br />
<br />
== Booking calendars ==<br />
Since some pieces of hardware are used intensively it is necessary to book them in advance. The links to the corresponding booking calendars are listed below.<br />
<ul><br />
<li><br />
Fluorescence microscopes<br />
<ul><br />
<li>[http://www.my.calendars.net/olympusszx16 Olympus SZX 16]</li><br />
<li>[http://www.my.calendars.net/new_olympus/ New Olympus SZX 16]</li><br />
<li>[http://www.my.calendars.net/Olympus_OVK Olympus OVK]</li><br />
<li>[http://www.my.calendars.net/axio_observer/ Axio Observer]</li><br />
</ul><br />
</li><br />
<li><br />
Microinjectors and electroporators and dissecting microscope<br />
<ul><br />
<li>Room 0.232<br />
<ul> <br />
<li>[http://www.my.calendars.net/electroporator Nepa Gene]</li><br />
<li>[http://www.my.calendars.net/electroporator2 ECM 830]</li><br />
<li>[http://www.my.calendars.net/stereoscope2/d01/11/2012 Olympus dissecting microscope]</li><br />
</ul><br />
</li><br />
<li>Lab<br />
<ul><br />
<li>[http://www.my.calendars.net/OlympusLab Olympus (next to the axolotls)]</li><br />
<li>[http://www.my.calendars.net/OlympusLab2 Olympus (next to the Microtome)]</li><br />
</ul><br />
</li><br />
</ul><br />
</li><br />
<li><br />
Confocal microscopes<br />
<ul><br />
<li>[http://www.my.calendars.net/leica_lsm Leica LSM]</li><br />
</ul><br />
</li><br />
<li><br />
Cryostats<br />
<ul><br />
<li>[http://www.my.calendars.net/cryostat1 Cryostat 1]</li><br />
<li>[http://www.my.calendars.net/cryostat2 Cryostat 2]</li><br />
</ul><br />
</li><br />
<li><br />
Microtome<br />
<ul><br />
<li>[http://www.my.calendars.net/microtome Microtome]</li><br />
</ul><br />
</li><br />
<li><br />
Paraffin embedding station<br />
<ul><br />
<li>[http://www.my.calendars.net/wax_station Paraffin embedding station]</li><br />
</ul><br />
</li><br />
</ul><br />
<br />
== Genetics ==<br />
=== Transgenic lines ===<br />
<ul><br />
<li>[[Transgenic_axolotl_lines|Axolotl (A.mexicanum)]]</li><br />
<li>[[Transgenic_frog_lines|Frog (X.laevis)]]</li><br />
</ul><br />
<br />
=== Markers ===<br />
{| class="wikitable sortable"<br />
!style="width: 150px" | Marker<br />
!style="width: 250px" | Full name<br />
!style="width: 250px" | Target<br />
!style="width: 450px" | Remarks<br />
|-<br />
|DAPI/Hoechst<br />
|<br />
|Nuclei<br />
|Incorporates into the DNA<br />
|-<br />
|PCNA<br />
|Proliferating-Cell-Nuclear-Antigen<br />
|Dividing cells<br />
|<br />
|-<br />
|Sox2<br />
|<br />
|Preferentially neuronal lineage<br />
|Progenitor marker for both spinal cord and brain<br />
|-<br />
|PAX6<br />
|<br />
|Brain, Spinal Cord<br />
|<br />
|-<br />
|PAX7<br />
|<br />
|Satellite cells, Spinal Cord, Brain<br />
|<br />
|-<br />
|MHC<br />
|Myosin heavy chain<br />
|Muscle fibers<br />
|<br />
|-<br />
|Myf5<br />
|<br />
|Muscle fibers<br />
|Labels cycling myoblasts<br />
|-<br />
|ßIII-tubulin<br />
|<br />
|Axons<br />
|<br />
|-<br />
|MBP<br />
|Myelin basic protein<br />
|Schwann cells<br />
|<br />
|-<br />
|Prrx1<br />
|<br />
|Blastema/mesodermal cells of limb bud<br />
|<br />
|-<br />
|SMA<br />
|<br />
|Blood vessels/endothelial cells<br />
|<br />
|-<br />
|GFAP<br />
|Glial fibrillary acidic protein<br />
|Glia<br />
|<br />
|-<br />
|NeuN<br />
|<br />
|Differentiated nerve<br />
|<br />
|-<br />
|Leu7<br />
|<br />
|Schwann cells<br />
|<br />
|-<br />
|Xbra<br />
|Xbrachyury<br />
|Mesoderm during gastrula stage<br />
|<br />
|-<br />
|Msx1<br />
|<br />
|Undifferentiated cells<br />
|Transcriptional repressor during embryogenesis<br />
|-<br />
|Trypan blue<br />
|<br />
|Dead tissues or cells<br />
|Vital stain<br />
|-<br />
|Mef2c<br />
|<br />
|Differentiated muscle cells<br />
|<br />
|-<br />
|PH3<br />
|<br />
|Mitotic cells<br />
|<br />
|-<br />
|BrdU<br />
|<br />
|Cells in S-phase<br />
|<br />
|-<br />
|Casp3<br />
|<br />
|Dying cells<br />
|<br />
|-<br />
|Gdf5<br />
|<br />
|Joints<br />
|Joint development marker<br />
|-<br />
|Survivin<br />
|<br />
|Cleavage furrow<br />
|<br />
|}<br />
<br />
== Digital data ==<br />
Over the years the members of the lab have produced a lot of different data: Sanger sequences, EST libraries, images and so on. <br />
Select a category from the list below in order to view or download the data.<br />
<br />
=== Fileservers ===<br />
{| class="wikitable"<br />
!style="width: 350px" | Location<br />
!style="width: 250px" | Volume size<br />
!style="width: 350px" | Description<br />
!style="width: 350px" | Access<br />
!style="width: 350px" | Location (console only)<br />
|-<br />
|//biodata/groups/<b>crtd_tanaka</b><br />
|16 TB<br />
|General purpose storage space<br />
|Entire Tanaka lab<br />
|<i>biocluster:</i> <b>/group/crtd_tanaka</b><br />
|-<br />
|//biodata/groups/<b>tanaka-ests</b><br />
|247 GB<br />
|EST sequences<br />
|Entire Tanaka lab<br />
|<i>biocluster:</i> <b>/group/tanaka-ests</b><br />
|-<br />
|//biodata/groups/<b>axolotl-transcriptome</b><br />
|500 GB<br />
|Axolotl transcriptome data<br />
|Elly, Sergej<br />
|<i>biocluster:</i> <b>/projects/axolotl-transcriptome</b><br />
|-<br />
|//biodata/groups/<b>tanaka-saori</b><br />
|878 GB<br />
|Special directory for Saori's data<br />
|Elly, Saori, Sergej<br />
|<i>biocluster:</i> <b>/group/tanaka-saori</b><br />
|}<br />
<br />
{{Tip|The path is different, when accessing the file server from the console.}}<br />
<br />
=== Literature ===<br />
<ul><br />
<li>[[Literature#Theses|Theses]]</li><br />
<li>[[Literature#Publications|Publications]]</li><br />
</ul><br />
<br />
=== Databases ===<br />
<ul><br />
<li>[http://est.age.mpg.de/axolotl/ Axolotl transcriptome] website contains the Axolotl transcriptome assemblies</li><br />
<li>[http://newtomics.mpi-bn.mpg.de/ Newt transcriptome] website contains the Newt transcriptome assembly</li><br />
<li>[http://sandberg.cmb.ki.se/redspottednewt/ Red spotted newt transcriptome] website contains the red spotted newt transcriptome assembly</li><br />
<li>[https://python-srv1.mpi-cbg.de/axolotl/cgi-bin/login.cgi Axolotl EST] database contains several ESTs and also some additional information, e.g. the position of the well with the corresponding insert in the Blastema (BL) or Neural tube (NT) library.</li><br />
<li>[http://est.age.mpg.de/ Axologle] database contains expression profiling data of Axolotl limb regeneration</li><br />
<li>[http://est.age.mpg.de/blast/blast.html Axolotl BLAST] database contains several different BLAST-able Axolotl transciptome assemblies</li><br />
</ul><br />
<br />
=== Datasets ===<br />
<ul><br />
<li>[[Datasets#Sequences|Sequences]]<br />
<ul><br />
<li>[[Datasets#Illumina|Illumina]]</li><br />
<li>[[Datasets#Sanger|Sanger]]</li><br />
<li>[[Datasets#Roche.2F454|Roche/454]]</li><br />
</ul><br />
</li><br />
<li>[[Datasets#Microarrays|Microarrays]]<br />
</ul><br />
<br />
=== Interesting links ===<br />
<ul><br />
<li>[http://www.nytimes.com/video/2013/02/27/science/100000002087758/finding-the-visible-in-the-invisible.html Visible in the invisible]: a movie introducing a new image processing ana analysis technique developed at the MIT.</li><br />
</ul><br />
<br />
== Lab life ==<br />
<ul><br />
<li>[[Lab_photos|Lab photos]]</li><br />
<li>Further pictures can be found in <b>/biodata/groups/crtd_tanaka/LabFun/</b></li><br />
<li>The recepies for Heino's farewell present can be found under <b>/biodata/groups/crtd_tanaka/LabFun/Heino's farewell present/</b></li><br />
<li>The video of the visit of the EU commissioner can be found under <b>/biodata/groups/crtd_tanaka/LabFun/</b></li><br />
</ul></div>
Serghein
https://wiki.tanakalab.org/index.php?title=Overview&diff=278
Overview
2013-07-16T10:13:43Z
<p>Serghein: /* Markers */</p>
<hr />
<div>== Introduction ==<br />
On the pages listed below you can find most common protocols used in the lab as well as a list of lab duties along with the names of the responsible persons. Please, contact the responsible persons if you have any question, suggestions or troubles.<br />
<br />
== Axolotl ==<br />
<br />
=== Maintainance ===<br />
In this section you will find some general information on how to [[Axolotl#Maintaining_the_axolotls|maintain]] the animals.<br />
<br />
=== Feeding ===<br />
This section will give you an overview of how to [[Axolotl#Feeding|feed]] the axolotls.<br />
<br />
=== Interesting observations ===<br />
In the following section you can find some [[Axolotl#Interesting_observations|interesting observations]] concerning the axolotl, its behavior, caveats of the transgenics and many more.<br />
<br />
== Lab duties ==<br />
<ul><br />
=== Chemicals ===<br />
<li>[[Antibiotics|Antibiotics]]</li><br />
<li>[[Benzocaine|Benzocaine]]</li><br />
<li>[[Fibronectin|Fibronectin]]</li><br />
<li>[[Gelatine|Gelatine]]</li><br />
<li>[[Liquid_nitrogen|Liquid nitrogen]]</li><br />
<li>[[Primary_antibodies|Primary antibodies]]</li><br />
<li>[[Secondary_antibodies|Secondary antibodies]]</li><br />
<li>[[Serum_immunostaining|Serum immunostaining]]</li><br />
<br />
=== Hardware ===<br />
<li>[[Autoclave|Autoclave]]</li><br />
<li>[[Cryostat|Cryostat]]</li><br />
<li>[[Dissecting_microscopes|Dissecting microscopes]]</li><br />
<li>[[Leica_confocal_microscope|Leica confocal microscope]]</li><br />
<li>[[Vacuum_pumps|Vacuum pumps]]</li><br />
<li>[[Waterbath|Waterbath]]</li><br />
<br />
=== General ===<br />
<li>[[Ordering_common_stuff|Ordering common stuff]]</li><br />
<li>[[Heat_shock_competent_cells|Heat-shock competent cells]]</li><br />
</ul><br />
<br />
<br />
== Protocols ==<br />
<ul><br />
=== Cell culture ===<br />
<li>[[Blastema_cells|Blastema cells]]</li><br />
<li>[[Baculovirus_titration|Baculovirus titration]]</li><br />
<li>[[Myoblasts_electroporation|Myoblasts electroporation]]</li><br />
<li>[[Adhesive_cell_culture|Adhesive cell culture]]</li><br />
<li>[[Electroporation_of_blastema_cells|Electroporation of blastema cells]]</li><br />
<li>[[Electroporation_of_nec|Electroporation of neural epithelia cells (axolotl spinal cord)]]</li><br />
<li>[[mESC_culture|mESC culture/Cyst formation]]</li><br />
<li>[[Neurosphere_culture|Neurosphere culture]]</li><br />
=== Histology ===<br />
<li>[[Double_Immunostaining_via_antigen_retrieval|Double Immunostaining via antigen retrieval (Sherry)]]</li><br />
=== Molecular biology ===<br />
<li>[[Metamorphosis_protocol|Metamorphosis protocol (Sherry)]]</li><br />
</ul><br />
<br />
== Booking calendars ==<br />
Since some pieces of hardware are used intensively it is necessary to book them in advance. The links to the corresponding booking calendars are listed below.<br />
<ul><br />
<li><br />
Fluorescence microscopes<br />
<ul><br />
<li>[http://www.my.calendars.net/olympusszx16 Olympus SZX 16]</li><br />
<li>[http://www.my.calendars.net/new_olympus/ New Olympus SZX 16]</li><br />
<li>[http://www.my.calendars.net/Olympus_OVK Olympus OVK]</li><br />
<li>[http://www.my.calendars.net/axio_observer/ Axio Observer]</li><br />
</ul><br />
</li><br />
<li><br />
Microinjectors and electroporators and dissecting microscope<br />
<ul><br />
<li>Room 0.232<br />
<ul> <br />
<li>[http://www.my.calendars.net/electroporator Nepa Gene]</li><br />
<li>[http://www.my.calendars.net/electroporator2 ECM 830]</li><br />
<li>[http://www.my.calendars.net/stereoscope2/d01/11/2012 Olympus dissecting microscope]</li><br />
</ul><br />
</li><br />
<li>Lab<br />
<ul><br />
<li>[http://www.my.calendars.net/OlympusLab Olympus (next to the axolotls)]</li><br />
<li>[http://www.my.calendars.net/OlympusLab2 Olympus (next to the Microtome)]</li><br />
</ul><br />
</li><br />
</ul><br />
</li><br />
<li><br />
Confocal microscopes<br />
<ul><br />
<li>[http://www.my.calendars.net/leica_lsm Leica LSM]</li><br />
</ul><br />
</li><br />
<li><br />
Cryostats<br />
<ul><br />
<li>[http://www.my.calendars.net/cryostat1 Cryostat 1]</li><br />
<li>[http://www.my.calendars.net/cryostat2 Cryostat 2]</li><br />
</ul><br />
</li><br />
<li><br />
Microtome<br />
<ul><br />
<li>[http://www.my.calendars.net/microtome Microtome]</li><br />
</ul><br />
</li><br />
<li><br />
Paraffin embedding station<br />
<ul><br />
<li>[http://www.my.calendars.net/wax_station Paraffin embedding station]</li><br />
</ul><br />
</li><br />
</ul><br />
<br />
== Genetics ==<br />
=== Transgenic lines ===<br />
<ul><br />
<li>[[Transgenic_axolotl_lines|Axolotl (A.mexicanum)]]</li><br />
<li>[[Transgenic_frog_lines|Frog (X.laevis)]]</li><br />
</ul><br />
<br />
=== Markers ===<br />
{| class="wikitable sortable"<br />
!style="width: 150px" | Marker<br />
!style="width: 250px" | Full name<br />
!style="width: 250px" | Target<br />
!style="width: 450px" | Remarks<br />
|-<br />
|DAPI/Hoechst<br />
|<br />
|Nuclei<br />
|Incorporates into the DNA<br />
|-<br />
|PCNA<br />
|Proliferating-Cell-Nuclear-Antigen<br />
|Dividing cells<br />
|<br />
|-<br />
|Sox2<br />
|<br />
|Preferentially neuronal lineage<br />
|Progenitor marker for both spinal cord and brain<br />
|-<br />
|PAX6<br />
|<br />
|Brain<br />
|<br />
|-<br />
|PAX7<br />
|<br />
|Satellite cells<br />
|<br />
|-<br />
|MHC<br />
|Myosin heavy chain<br />
|Muscle fibers<br />
|<br />
|-<br />
|Myf5<br />
|<br />
|Muscle fibers<br />
|Labels cycling myoblasts<br />
|-<br />
|ß3 tubulin<br />
|<br />
|Axons<br />
|<br />
|-<br />
|MBP<br />
|Myelin basic protein<br />
|Schwann cells<br />
|<br />
|-<br />
|Prrx1<br />
|<br />
|Blastema/mesodermal cells of limb bud<br />
|<br />
|-<br />
|SMA<br />
|<br />
|Blood vessels/endothelial cells<br />
|<br />
|-<br />
|GFAP<br />
|Glial fibrillary acidic protein<br />
|Glia<br />
|<br />
|-<br />
|NeuN<br />
|<br />
|Differentiated nerve<br />
|<br />
|-<br />
|Leu7<br />
|<br />
|Schwann cells<br />
|<br />
|-<br />
|Xbra<br />
|Xbrachyury<br />
|Mesoderm during gastrula stage<br />
|<br />
|-<br />
|Msx1<br />
|<br />
|Undifferentiated cells<br />
|Transcriptional repressor during embryogenesis<br />
|-<br />
|Trypan blue<br />
|<br />
|Dead tissues or cells<br />
|Vital stain<br />
|-<br />
|Mef2c<br />
|<br />
|Differentiated muscle cells<br />
|<br />
|-<br />
|PH3<br />
|<br />
|Mitotic cells<br />
|<br />
|-<br />
|BrdU<br />
|<br />
|Cells in S-phase<br />
|<br />
|-<br />
|Casp3<br />
|<br />
|Dying cells<br />
|<br />
|-<br />
|Gdf5<br />
|<br />
|Joints<br />
|Joint development marker<br />
|-<br />
|Survivin<br />
|<br />
|Cleavage furrow<br />
|<br />
|}<br />
<br />
== Digital data ==<br />
Over the years the members of the lab have produced a lot of different data: Sanger sequences, EST libraries, images and so on. <br />
Select a category from the list below in order to view or download the data.<br />
<br />
=== Fileservers ===<br />
{| class="wikitable"<br />
!style="width: 350px" | Location<br />
!style="width: 250px" | Volume size<br />
!style="width: 350px" | Description<br />
!style="width: 350px" | Access<br />
!style="width: 350px" | Location (console only)<br />
|-<br />
|//biodata/groups/<b>crtd_tanaka</b><br />
|16 TB<br />
|General purpose storage space<br />
|Entire Tanaka lab<br />
|<i>biocluster:</i> <b>/group/crtd_tanaka</b><br />
|-<br />
|//biodata/groups/<b>tanaka-ests</b><br />
|247 GB<br />
|EST sequences<br />
|Entire Tanaka lab<br />
|<i>biocluster:</i> <b>/group/tanaka-ests</b><br />
|-<br />
|//biodata/groups/<b>axolotl-transcriptome</b><br />
|500 GB<br />
|Axolotl transcriptome data<br />
|Elly, Sergej<br />
|<i>biocluster:</i> <b>/projects/axolotl-transcriptome</b><br />
|-<br />
|//biodata/groups/<b>tanaka-saori</b><br />
|878 GB<br />
|Special directory for Saori's data<br />
|Elly, Saori, Sergej<br />
|<i>biocluster:</i> <b>/group/tanaka-saori</b><br />
|}<br />
<br />
{{Tip|The path is different, when accessing the file server from the console.}}<br />
<br />
=== Literature ===<br />
<ul><br />
<li>[[Literature#Theses|Theses]]</li><br />
<li>[[Literature#Publications|Publications]]</li><br />
</ul><br />
<br />
=== Databases ===<br />
<ul><br />
<li>[http://est.age.mpg.de/axolotl/ Axolotl transcriptome] website contains the Axolotl transcriptome assemblies</li><br />
<li>[http://newtomics.mpi-bn.mpg.de/ Newt transcriptome] website contains the Newt transcriptome assembly</li><br />
<li>[http://sandberg.cmb.ki.se/redspottednewt/ Red spotted newt transcriptome] website contains the red spotted newt transcriptome assembly</li><br />
<li>[https://python-srv1.mpi-cbg.de/axolotl/cgi-bin/login.cgi Axolotl EST] database contains several ESTs and also some additional information, e.g. the position of the well with the corresponding insert in the Blastema (BL) or Neural tube (NT) library.</li><br />
<li>[http://est.age.mpg.de/ Axologle] database contains expression profiling data of Axolotl limb regeneration</li><br />
<li>[http://est.age.mpg.de/blast/blast.html Axolotl BLAST] database contains several different BLAST-able Axolotl transciptome assemblies</li><br />
</ul><br />
<br />
=== Datasets ===<br />
<ul><br />
<li>[[Datasets#Sequences|Sequences]]<br />
<ul><br />
<li>[[Datasets#Illumina|Illumina]]</li><br />
<li>[[Datasets#Sanger|Sanger]]</li><br />
<li>[[Datasets#Roche.2F454|Roche/454]]</li><br />
</ul><br />
</li><br />
<li>[[Datasets#Microarrays|Microarrays]]<br />
</ul><br />
<br />
=== Interesting links ===<br />
<ul><br />
<li>[http://www.nytimes.com/video/2013/02/27/science/100000002087758/finding-the-visible-in-the-invisible.html Visible in the invisible]: a movie introducing a new image processing ana analysis technique developed at the MIT.</li><br />
</ul><br />
<br />
== Lab life ==<br />
<ul><br />
<li>[[Lab_photos|Lab photos]]</li><br />
<li>Further pictures can be found in <b>/biodata/groups/crtd_tanaka/LabFun/</b></li><br />
<li>The recepies for Heino's farewell present can be found under <b>/biodata/groups/crtd_tanaka/LabFun/Heino's farewell present/</b></li><br />
<li>The video of the visit of the EU commissioner can be found under <b>/biodata/groups/crtd_tanaka/LabFun/</b></li><br />
</ul></div>
Serghein
https://wiki.tanakalab.org/index.php?title=Overview&diff=277
Overview
2013-07-16T10:06:50Z
<p>Serghein: /* Markers */</p>
<hr />
<div>== Introduction ==<br />
On the pages listed below you can find most common protocols used in the lab as well as a list of lab duties along with the names of the responsible persons. Please, contact the responsible persons if you have any question, suggestions or troubles.<br />
<br />
== Axolotl ==<br />
<br />
=== Maintainance ===<br />
In this section you will find some general information on how to [[Axolotl#Maintaining_the_axolotls|maintain]] the animals.<br />
<br />
=== Feeding ===<br />
This section will give you an overview of how to [[Axolotl#Feeding|feed]] the axolotls.<br />
<br />
=== Interesting observations ===<br />
In the following section you can find some [[Axolotl#Interesting_observations|interesting observations]] concerning the axolotl, its behavior, caveats of the transgenics and many more.<br />
<br />
== Lab duties ==<br />
<ul><br />
=== Chemicals ===<br />
<li>[[Antibiotics|Antibiotics]]</li><br />
<li>[[Benzocaine|Benzocaine]]</li><br />
<li>[[Fibronectin|Fibronectin]]</li><br />
<li>[[Gelatine|Gelatine]]</li><br />
<li>[[Liquid_nitrogen|Liquid nitrogen]]</li><br />
<li>[[Primary_antibodies|Primary antibodies]]</li><br />
<li>[[Secondary_antibodies|Secondary antibodies]]</li><br />
<li>[[Serum_immunostaining|Serum immunostaining]]</li><br />
<br />
=== Hardware ===<br />
<li>[[Autoclave|Autoclave]]</li><br />
<li>[[Cryostat|Cryostat]]</li><br />
<li>[[Dissecting_microscopes|Dissecting microscopes]]</li><br />
<li>[[Leica_confocal_microscope|Leica confocal microscope]]</li><br />
<li>[[Vacuum_pumps|Vacuum pumps]]</li><br />
<li>[[Waterbath|Waterbath]]</li><br />
<br />
=== General ===<br />
<li>[[Ordering_common_stuff|Ordering common stuff]]</li><br />
<li>[[Heat_shock_competent_cells|Heat-shock competent cells]]</li><br />
</ul><br />
<br />
<br />
== Protocols ==<br />
<ul><br />
=== Cell culture ===<br />
<li>[[Blastema_cells|Blastema cells]]</li><br />
<li>[[Baculovirus_titration|Baculovirus titration]]</li><br />
<li>[[Myoblasts_electroporation|Myoblasts electroporation]]</li><br />
<li>[[Adhesive_cell_culture|Adhesive cell culture]]</li><br />
<li>[[Electroporation_of_blastema_cells|Electroporation of blastema cells]]</li><br />
<li>[[Electroporation_of_nec|Electroporation of neural epithelia cells (axolotl spinal cord)]]</li><br />
<li>[[mESC_culture|mESC culture/Cyst formation]]</li><br />
<li>[[Neurosphere_culture|Neurosphere culture]]</li><br />
=== Histology ===<br />
<li>[[Double_Immunostaining_via_antigen_retrieval|Double Immunostaining via antigen retrieval (Sherry)]]</li><br />
=== Molecular biology ===<br />
<li>[[Metamorphosis_protocol|Metamorphosis protocol (Sherry)]]</li><br />
</ul><br />
<br />
== Booking calendars ==<br />
Since some pieces of hardware are used intensively it is necessary to book them in advance. The links to the corresponding booking calendars are listed below.<br />
<ul><br />
<li><br />
Fluorescence microscopes<br />
<ul><br />
<li>[http://www.my.calendars.net/olympusszx16 Olympus SZX 16]</li><br />
<li>[http://www.my.calendars.net/new_olympus/ New Olympus SZX 16]</li><br />
<li>[http://www.my.calendars.net/Olympus_OVK Olympus OVK]</li><br />
<li>[http://www.my.calendars.net/axio_observer/ Axio Observer]</li><br />
</ul><br />
</li><br />
<li><br />
Microinjectors and electroporators and dissecting microscope<br />
<ul><br />
<li>Room 0.232<br />
<ul> <br />
<li>[http://www.my.calendars.net/electroporator Nepa Gene]</li><br />
<li>[http://www.my.calendars.net/electroporator2 ECM 830]</li><br />
<li>[http://www.my.calendars.net/stereoscope2/d01/11/2012 Olympus dissecting microscope]</li><br />
</ul><br />
</li><br />
<li>Lab<br />
<ul><br />
<li>[http://www.my.calendars.net/OlympusLab Olympus (next to the axolotls)]</li><br />
<li>[http://www.my.calendars.net/OlympusLab2 Olympus (next to the Microtome)]</li><br />
</ul><br />
</li><br />
</ul><br />
</li><br />
<li><br />
Confocal microscopes<br />
<ul><br />
<li>[http://www.my.calendars.net/leica_lsm Leica LSM]</li><br />
</ul><br />
</li><br />
<li><br />
Cryostats<br />
<ul><br />
<li>[http://www.my.calendars.net/cryostat1 Cryostat 1]</li><br />
<li>[http://www.my.calendars.net/cryostat2 Cryostat 2]</li><br />
</ul><br />
</li><br />
<li><br />
Microtome<br />
<ul><br />
<li>[http://www.my.calendars.net/microtome Microtome]</li><br />
</ul><br />
</li><br />
<li><br />
Paraffin embedding station<br />
<ul><br />
<li>[http://www.my.calendars.net/wax_station Paraffin embedding station]</li><br />
</ul><br />
</li><br />
</ul><br />
<br />
== Genetics ==<br />
=== Transgenic lines ===<br />
<ul><br />
<li>[[Transgenic_axolotl_lines|Axolotl (A.mexicanum)]]</li><br />
<li>[[Transgenic_frog_lines|Frog (X.laevis)]]</li><br />
</ul><br />
<br />
=== Markers ===<br />
{| class="wikitable sortable"<br />
!style="width: 150px" | Marker<br />
!style="width: 250px" | Full name<br />
!style="width: 250px" | Target<br />
!style="width: 450px" | Remarks<br />
|-<br />
|DAPI/Hoechst<br />
|<br />
|Nuclei<br />
|Incorporates into the DNA<br />
|-<br />
|PCNA<br />
|Proliferating-Cell-Nuclear-Antigen<br />
|Dividing cells<br />
|<br />
|-<br />
|Sox2<br />
|<br />
|Preferentially neuronal lineage<br />
|Progenitor marker for both spinal cord and brain<br />
|-<br />
|PAX6<br />
|<br />
|Brain<br />
|<br />
|-<br />
|PAX7<br />
|<br />
|Satellite cells<br />
|<br />
|-<br />
|MHC<br />
|Myosin heavy chain<br />
|Muscle fibers<br />
|<br />
|-<br />
|Myf5<br />
|<br />
|Muscle fibers<br />
|Labels cycling myoblasts<br />
|}<br />
<br />
== Digital data ==<br />
Over the years the members of the lab have produced a lot of different data: Sanger sequences, EST libraries, images and so on. <br />
Select a category from the list below in order to view or download the data.<br />
<br />
=== Fileservers ===<br />
{| class="wikitable"<br />
!style="width: 350px" | Location<br />
!style="width: 250px" | Volume size<br />
!style="width: 350px" | Description<br />
!style="width: 350px" | Access<br />
!style="width: 350px" | Location (console only)<br />
|-<br />
|//biodata/groups/<b>crtd_tanaka</b><br />
|16 TB<br />
|General purpose storage space<br />
|Entire Tanaka lab<br />
|<i>biocluster:</i> <b>/group/crtd_tanaka</b><br />
|-<br />
|//biodata/groups/<b>tanaka-ests</b><br />
|247 GB<br />
|EST sequences<br />
|Entire Tanaka lab<br />
|<i>biocluster:</i> <b>/group/tanaka-ests</b><br />
|-<br />
|//biodata/groups/<b>axolotl-transcriptome</b><br />
|500 GB<br />
|Axolotl transcriptome data<br />
|Elly, Sergej<br />
|<i>biocluster:</i> <b>/projects/axolotl-transcriptome</b><br />
|-<br />
|//biodata/groups/<b>tanaka-saori</b><br />
|878 GB<br />
|Special directory for Saori's data<br />
|Elly, Saori, Sergej<br />
|<i>biocluster:</i> <b>/group/tanaka-saori</b><br />
|}<br />
<br />
{{Tip|The path is different, when accessing the file server from the console.}}<br />
<br />
=== Literature ===<br />
<ul><br />
<li>[[Literature#Theses|Theses]]</li><br />
<li>[[Literature#Publications|Publications]]</li><br />
</ul><br />
<br />
=== Databases ===<br />
<ul><br />
<li>[http://est.age.mpg.de/axolotl/ Axolotl transcriptome] website contains the Axolotl transcriptome assemblies</li><br />
<li>[http://newtomics.mpi-bn.mpg.de/ Newt transcriptome] website contains the Newt transcriptome assembly</li><br />
<li>[http://sandberg.cmb.ki.se/redspottednewt/ Red spotted newt transcriptome] website contains the red spotted newt transcriptome assembly</li><br />
<li>[https://python-srv1.mpi-cbg.de/axolotl/cgi-bin/login.cgi Axolotl EST] database contains several ESTs and also some additional information, e.g. the position of the well with the corresponding insert in the Blastema (BL) or Neural tube (NT) library.</li><br />
<li>[http://est.age.mpg.de/ Axologle] database contains expression profiling data of Axolotl limb regeneration</li><br />
<li>[http://est.age.mpg.de/blast/blast.html Axolotl BLAST] database contains several different BLAST-able Axolotl transciptome assemblies</li><br />
</ul><br />
<br />
=== Datasets ===<br />
<ul><br />
<li>[[Datasets#Sequences|Sequences]]<br />
<ul><br />
<li>[[Datasets#Illumina|Illumina]]</li><br />
<li>[[Datasets#Sanger|Sanger]]</li><br />
<li>[[Datasets#Roche.2F454|Roche/454]]</li><br />
</ul><br />
</li><br />
<li>[[Datasets#Microarrays|Microarrays]]<br />
</ul><br />
<br />
=== Interesting links ===<br />
<ul><br />
<li>[http://www.nytimes.com/video/2013/02/27/science/100000002087758/finding-the-visible-in-the-invisible.html Visible in the invisible]: a movie introducing a new image processing ana analysis technique developed at the MIT.</li><br />
</ul><br />
<br />
== Lab life ==<br />
<ul><br />
<li>[[Lab_photos|Lab photos]]</li><br />
<li>Further pictures can be found in <b>/biodata/groups/crtd_tanaka/LabFun/</b></li><br />
<li>The recepies for Heino's farewell present can be found under <b>/biodata/groups/crtd_tanaka/LabFun/Heino's farewell present/</b></li><br />
<li>The video of the visit of the EU commissioner can be found under <b>/biodata/groups/crtd_tanaka/LabFun/</b></li><br />
</ul></div>
Serghein
https://wiki.tanakalab.org/index.php?title=Overview&diff=276
Overview
2013-07-16T09:58:51Z
<p>Serghein: </p>
<hr />
<div>== Introduction ==<br />
On the pages listed below you can find most common protocols used in the lab as well as a list of lab duties along with the names of the responsible persons. Please, contact the responsible persons if you have any question, suggestions or troubles.<br />
<br />
== Axolotl ==<br />
<br />
=== Maintainance ===<br />
In this section you will find some general information on how to [[Axolotl#Maintaining_the_axolotls|maintain]] the animals.<br />
<br />
=== Feeding ===<br />
This section will give you an overview of how to [[Axolotl#Feeding|feed]] the axolotls.<br />
<br />
=== Interesting observations ===<br />
In the following section you can find some [[Axolotl#Interesting_observations|interesting observations]] concerning the axolotl, its behavior, caveats of the transgenics and many more.<br />
<br />
== Lab duties ==<br />
<ul><br />
=== Chemicals ===<br />
<li>[[Antibiotics|Antibiotics]]</li><br />
<li>[[Benzocaine|Benzocaine]]</li><br />
<li>[[Fibronectin|Fibronectin]]</li><br />
<li>[[Gelatine|Gelatine]]</li><br />
<li>[[Liquid_nitrogen|Liquid nitrogen]]</li><br />
<li>[[Primary_antibodies|Primary antibodies]]</li><br />
<li>[[Secondary_antibodies|Secondary antibodies]]</li><br />
<li>[[Serum_immunostaining|Serum immunostaining]]</li><br />
<br />
=== Hardware ===<br />
<li>[[Autoclave|Autoclave]]</li><br />
<li>[[Cryostat|Cryostat]]</li><br />
<li>[[Dissecting_microscopes|Dissecting microscopes]]</li><br />
<li>[[Leica_confocal_microscope|Leica confocal microscope]]</li><br />
<li>[[Vacuum_pumps|Vacuum pumps]]</li><br />
<li>[[Waterbath|Waterbath]]</li><br />
<br />
=== General ===<br />
<li>[[Ordering_common_stuff|Ordering common stuff]]</li><br />
<li>[[Heat_shock_competent_cells|Heat-shock competent cells]]</li><br />
</ul><br />
<br />
<br />
== Protocols ==<br />
<ul><br />
=== Cell culture ===<br />
<li>[[Blastema_cells|Blastema cells]]</li><br />
<li>[[Baculovirus_titration|Baculovirus titration]]</li><br />
<li>[[Myoblasts_electroporation|Myoblasts electroporation]]</li><br />
<li>[[Adhesive_cell_culture|Adhesive cell culture]]</li><br />
<li>[[Electroporation_of_blastema_cells|Electroporation of blastema cells]]</li><br />
<li>[[Electroporation_of_nec|Electroporation of neural epithelia cells (axolotl spinal cord)]]</li><br />
<li>[[mESC_culture|mESC culture/Cyst formation]]</li><br />
<li>[[Neurosphere_culture|Neurosphere culture]]</li><br />
=== Histology ===<br />
<li>[[Double_Immunostaining_via_antigen_retrieval|Double Immunostaining via antigen retrieval (Sherry)]]</li><br />
=== Molecular biology ===<br />
<li>[[Metamorphosis_protocol|Metamorphosis protocol (Sherry)]]</li><br />
</ul><br />
<br />
== Booking calendars ==<br />
Since some pieces of hardware are used intensively it is necessary to book them in advance. The links to the corresponding booking calendars are listed below.<br />
<ul><br />
<li><br />
Fluorescence microscopes<br />
<ul><br />
<li>[http://www.my.calendars.net/olympusszx16 Olympus SZX 16]</li><br />
<li>[http://www.my.calendars.net/new_olympus/ New Olympus SZX 16]</li><br />
<li>[http://www.my.calendars.net/Olympus_OVK Olympus OVK]</li><br />
<li>[http://www.my.calendars.net/axio_observer/ Axio Observer]</li><br />
</ul><br />
</li><br />
<li><br />
Microinjectors and electroporators and dissecting microscope<br />
<ul><br />
<li>Room 0.232<br />
<ul> <br />
<li>[http://www.my.calendars.net/electroporator Nepa Gene]</li><br />
<li>[http://www.my.calendars.net/electroporator2 ECM 830]</li><br />
<li>[http://www.my.calendars.net/stereoscope2/d01/11/2012 Olympus dissecting microscope]</li><br />
</ul><br />
</li><br />
<li>Lab<br />
<ul><br />
<li>[http://www.my.calendars.net/OlympusLab Olympus (next to the axolotls)]</li><br />
<li>[http://www.my.calendars.net/OlympusLab2 Olympus (next to the Microtome)]</li><br />
</ul><br />
</li><br />
</ul><br />
</li><br />
<li><br />
Confocal microscopes<br />
<ul><br />
<li>[http://www.my.calendars.net/leica_lsm Leica LSM]</li><br />
</ul><br />
</li><br />
<li><br />
Cryostats<br />
<ul><br />
<li>[http://www.my.calendars.net/cryostat1 Cryostat 1]</li><br />
<li>[http://www.my.calendars.net/cryostat2 Cryostat 2]</li><br />
</ul><br />
</li><br />
<li><br />
Microtome<br />
<ul><br />
<li>[http://www.my.calendars.net/microtome Microtome]</li><br />
</ul><br />
</li><br />
<li><br />
Paraffin embedding station<br />
<ul><br />
<li>[http://www.my.calendars.net/wax_station Paraffin embedding station]</li><br />
</ul><br />
</li><br />
</ul><br />
<br />
== Genetics ==<br />
=== Transgenic lines ===<br />
<ul><br />
<li>[[Transgenic_axolotl_lines|Axolotl (A.mexicanum)]]</li><br />
<li>[[Transgenic_frog_lines|Frog (X.laevis)]]</li><br />
</ul><br />
<br />
=== Markers ===<br />
{| class="wikitable"<br />
!style="width: 150px" | Marker<br />
!style="width: 250px" | Full name<br />
!style="width: 250px" | Target<br />
!style="width: 450px" | Remarks<br />
|-<br />
|PCNA<br />
|Proliferating-Cell-Nuclear-Antigen<br />
|Dividing cells<br />
|<br />
|}<br />
<br />
== Digital data ==<br />
Over the years the members of the lab have produced a lot of different data: Sanger sequences, EST libraries, images and so on. <br />
Select a category from the list below in order to view or download the data.<br />
<br />
=== Fileservers ===<br />
{| class="wikitable"<br />
!style="width: 350px" | Location<br />
!style="width: 250px" | Volume size<br />
!style="width: 350px" | Description<br />
!style="width: 350px" | Access<br />
!style="width: 350px" | Location (console only)<br />
|-<br />
|//biodata/groups/<b>crtd_tanaka</b><br />
|16 TB<br />
|General purpose storage space<br />
|Entire Tanaka lab<br />
|<i>biocluster:</i> <b>/group/crtd_tanaka</b><br />
|-<br />
|//biodata/groups/<b>tanaka-ests</b><br />
|247 GB<br />
|EST sequences<br />
|Entire Tanaka lab<br />
|<i>biocluster:</i> <b>/group/tanaka-ests</b><br />
|-<br />
|//biodata/groups/<b>axolotl-transcriptome</b><br />
|500 GB<br />
|Axolotl transcriptome data<br />
|Elly, Sergej<br />
|<i>biocluster:</i> <b>/projects/axolotl-transcriptome</b><br />
|-<br />
|//biodata/groups/<b>tanaka-saori</b><br />
|878 GB<br />
|Special directory for Saori's data<br />
|Elly, Saori, Sergej<br />
|<i>biocluster:</i> <b>/group/tanaka-saori</b><br />
|}<br />
<br />
{{Tip|The path is different, when accessing the file server from the console.}}<br />
<br />
=== Literature ===<br />
<ul><br />
<li>[[Literature#Theses|Theses]]</li><br />
<li>[[Literature#Publications|Publications]]</li><br />
</ul><br />
<br />
=== Databases ===<br />
<ul><br />
<li>[http://est.age.mpg.de/axolotl/ Axolotl transcriptome] website contains the Axolotl transcriptome assemblies</li><br />
<li>[http://newtomics.mpi-bn.mpg.de/ Newt transcriptome] website contains the Newt transcriptome assembly</li><br />
<li>[http://sandberg.cmb.ki.se/redspottednewt/ Red spotted newt transcriptome] website contains the red spotted newt transcriptome assembly</li><br />
<li>[https://python-srv1.mpi-cbg.de/axolotl/cgi-bin/login.cgi Axolotl EST] database contains several ESTs and also some additional information, e.g. the position of the well with the corresponding insert in the Blastema (BL) or Neural tube (NT) library.</li><br />
<li>[http://est.age.mpg.de/ Axologle] database contains expression profiling data of Axolotl limb regeneration</li><br />
<li>[http://est.age.mpg.de/blast/blast.html Axolotl BLAST] database contains several different BLAST-able Axolotl transciptome assemblies</li><br />
</ul><br />
<br />
=== Datasets ===<br />
<ul><br />
<li>[[Datasets#Sequences|Sequences]]<br />
<ul><br />
<li>[[Datasets#Illumina|Illumina]]</li><br />
<li>[[Datasets#Sanger|Sanger]]</li><br />
<li>[[Datasets#Roche.2F454|Roche/454]]</li><br />
</ul><br />
</li><br />
<li>[[Datasets#Microarrays|Microarrays]]<br />
</ul><br />
<br />
=== Interesting links ===<br />
<ul><br />
<li>[http://www.nytimes.com/video/2013/02/27/science/100000002087758/finding-the-visible-in-the-invisible.html Visible in the invisible]: a movie introducing a new image processing ana analysis technique developed at the MIT.</li><br />
</ul><br />
<br />
== Lab life ==<br />
<ul><br />
<li>[[Lab_photos|Lab photos]]</li><br />
<li>Further pictures can be found in <b>/biodata/groups/crtd_tanaka/LabFun/</b></li><br />
<li>The recepies for Heino's farewell present can be found under <b>/biodata/groups/crtd_tanaka/LabFun/Heino's farewell present/</b></li><br />
<li>The video of the visit of the EU commissioner can be found under <b>/biodata/groups/crtd_tanaka/LabFun/</b></li><br />
</ul></div>
Serghein
https://wiki.tanakalab.org/index.php?title=Datasets&diff=275
Datasets
2013-06-30T16:43:32Z
<p>Serghein: /* Sanger */</p>
<hr />
<div>== Sequences ==<br />
=== Illumina ===<br />
The data can be found under <b>//biodata/groups/axolotl-transcriptome/raw/Illumina</b>.<br />
{| class="wikitable sortable"<br />
!style="width: 200px" class="unsortable" | Name<br />
!style="width: 300px" class="unsortable" | Description<br />
!style="width: 200px" | Tissue<br />
!style="width: 90px" class="unsortable" | Type<br />
!style="width: 80px" class="unsortable" | Read length<br />
!style="width: 100px" class="unsortable"| Fragment size<br />
!style="width: 150px" | Reads<br />
!style="width: 100px" class="unsortable" | Format<br />
!style="width: 200px" class="unsortable" | Location<br />
!style="width: 100px" | Author<br />
!style="width: 300px" class="unsortable" | Remarks<br />
|-<br />
|Mature spinal cord<br />
|Mature axolotl spinal cord<br />
|Spinal cord<br />
|Paired-ended<br />
|100bp<br />
|200-250bp<br />
|65,753,941<br />
|FastQ<br />
|SpinalCord/mSC.fastq.tar.gz<br />
|Akira Tazaki<br />
|<br />
|- <br />
|Injured spinal cord<br />
|Injured axolotl spinal cord, 6dpi<br />
|Spinal cord<br />
|Paired-ended<br />
|100bp<br />
|200-250bp<br />
|78,459,950<br />
|FastQ<br />
|SpinalCord/6diSC.fastq.tar.gz<br />
|Akira Tazaki<br />
|<br />
|-<br />
|Mature spinal cord<br />
|Mature axolotl spinal cord, replicate 2, crossing 142x5<br />
|Spinal cord<br />
|Paired-ended<br />
|100bp<br />
|180bp<br />
|101,769,559<br />
|FastQ<br />
|SpinalCord/mSC_142x5.fastq.tar.gz<br />
|Akira Tazaki<br />
|Due to a sequencer failure only the first 66 bases are safe<br />
|- <br />
|Mature spinal cord<br />
|Mature axolotl spinal cord, replicate 3, crossing 96x6<br />
|Spinal cord<br />
|Paired-ended<br />
|100bp<br />
|180bp<br />
|95,946,545<br />
|FastQ<br />
|SpinalCord/mSC_96x6.fastq.tar.gz<br />
|Akira Tazaki<br />
|Due to a sequencer failure only the first 66 bases are safe<br />
|- <br />
|Injured spinal cord<br />
|Injured axolotl spinal cord, 6dpi, replicate 2, crossing 142x5<br />
|Spinal cord<br />
|Paired-ended<br />
|100bp<br />
|180bp<br />
|96,626,387<br />
|FastQ<br />
|SpinalCord/6diSC_142x5.fastq.tar.gz<br />
|Akira Tazaki<br />
|Due to a sequencer failure only the first 66 bases are safe<br />
|- <br />
|Injured spinal cord<br />
|Injured axolotl spinal cord, 6dpi, replicate 3, crossing 96x5<br />
|Spinal cord<br />
|Paired-ended<br />
|100bp<br />
|180bp<br />
|99,855,603<br />
|FastQ<br />
|SpinalCord/6diSC_96x5.fastq.tar.gz<br />
|Akira Tazaki<br />
|Due to a sequencer failure only the first 66 bases are safe<br />
|-<br />
|Mature limb<br />
|Mature axolotl forelimb<br />
|Limb<br />
|Single-ended<br />
|76bp<br />
|n/a<br />
|65,934,228<br />
|FastQ<br />
|Limb/Mature.fastq.tar.gz<br />
|Dunja Knapp<br />
|<br />
|-<br />
|Amputated limb (36h)<br />
|Amputated axolotl forelimb (36hpa)<br />
|Limb<br />
|Single-ended<br />
|76bp<br />
|n/a<br />
|65,250,768<br />
|FastQ<br />
|Limb/36h_amp.fastq.tar.gz<br />
|Dunja Knapp<br />
|<br />
|-<br />
|Amputated limb (72h)<br />
|Amputated axolotl forelimb (72hpa)<br />
|Limb<br />
|Single-ended<br />
|76bp<br />
|n/a<br />
|62,970,898<br />
|FastQ<br />
|Limb/72h_amp.fastq.tar.gz<br />
|Dunja Knapp<br />
|<br />
|-<br />
|Lateral wound (36h)<br />
|Injured (lateral wound) axolotl forelimb (36hpw)<br />
|Limb<br />
|Single-ended<br />
|76bp<br />
|n/a<br />
|66,361,470<br />
|FastQ<br />
|Limb/36h_lw.fastq.tar.gz<br />
|Dunja Knapp<br />
|<br />
|-<br />
|Lateral wound (72h)<br />
|Injured (lateral wound) axolotl forelimb (72hpw)<br />
|Limb<br />
|Single-ended<br />
|76bp<br />
|n/a<br />
|64,133,834<br />
|FastQ<br />
|Limb/72h_lw.fastq.tar.gz<br />
|Dunja Knapp<br />
|<br />
|-<br />
|LPM-transplant<br />
|Blastema samples of a LPM-transplanted animal: mature and 1dpa<br />
|Limb blastema<br />
|Single-ended<br />
|<br />
|180bp<br />
|<ul><li>Mature: 35,982,029</li><li>1dpa: 39,824,276</li></ul><br />
|FastQ<br />
|LPM/An3.fastq.tar.gz<br />
|Prayag Murawala/Dunja Knapp<br />
|GFP-labeled LPM was transplanted to a white-host embryo. The limb of the host was amputated and the blastema sample was collected.<br />
|-<br />
|LPM-transplant<br />
|Blastema samples of a LPM-transplanted animal: mature and 10dpa<br />
|Limb blastema<br />
|Single-ended<br />
|<br />
|180bp<br />
|<ul><li>Mature: 47,155,937</li><li>10dpa: 40,468,959</li></ul><br />
|FastQ<br />
|LPM/An4.fastq.tar.gz<br />
|Prayag Murawala/Dunja Knapp<br />
|GFP-labeled LPM was transplanted to a white-host embryo. The limb of the host was amputated and the blastema sample was collected.<br />
|-<br />
|LPM-transplant<br />
|Blastema samples of a LPM-transplanted animal: mature and 5dpa<br />
|Limb blastema<br />
|Single-ended<br />
|<br />
|180bp<br />
|<ul><li>Mature: 38,879,295</li><li>5dpa: 33,775,319</li></ul><br />
|FastQ<br />
|LPM/An6.fastq.tar.gz<br />
|Prayag Murawala/Dunja Knapp<br />
|GFP-labeled LPM was transplanted to a white-host embryo. The limb of the host was amputated and the blastema sample was collected.<br />
|-<br />
|LPM-transplant<br />
|Blastema samples of a LPM-transplanted animal: mature and 7dpa<br />
|Limb blastema<br />
|Single-ended<br />
|<br />
|180bp<br />
|<ul><li>Mature: 52,385,146</li><li>7dpa: 54,639,187</li></ul><br />
|FastQ<br />
|LPM/An7.fastq.tar.gz<br />
|Prayag Murawala/Dunja Knapp<br />
|GFP-labeled LPM was transplanted to a white-host embryo. The limb of the host was amputated and the blastema sample was collected. <br />
|-<br />
|LPM-transplant<br />
|Blastema samples of a LPM-transplanted animal: mature and 3dpa<br />
|Limb blastema<br />
|Single-ended<br />
|<br />
|180bp<br />
|<ul><li>Mature: 69,327,682</li><li>3dpa: 52,633,592</li></ul><br />
|FastQ<br />
|LPM/An8.fastq.tar.gz<br />
|Prayag Murawala/Dunja Knapp<br />
|GFP-labeled LPM was transplanted to a white-host embryo. The limb of the host was amputated and the blastema sample was collected.<br />
|}<br />
<br />
Unsorted Illumina data can be found under <b>//biodata/groups/crtd_tanaka/LabData/Sequencing/Illumina/unsorted</b>.<br /><br />
For some of the data sets quality check was performed using FastQC. The statistics can be found under <b>//biodata/groups/crtd_tanaka/LabData/Sequencing/Illumina/qualitycheck</b>.<br />
<br />
=== Sanger ===<br />
The data can be found under <b>//biodata/groups/axolotl-transcriptome/raw/Sanger</b>.<br />
{| class="wikitable sortable"<br />
!style="width: 200px" class="unsortable" | Name<br />
!style="width: 300px" class="unsortable" | Description<br />
!style="width: 200px" | Tissue<br />
!style="width: 200px" | Sequences<br />
!style="width: 300px" class="unsortable" | Location<br />
!style="width: 100px" | Author<br />
!style="width: 300px" class="unsortable" | Remarks<br />
|-<br />
|LimbBlastema<br />
|Limb blastema library<br />
|Limb blastema<br />
|20160 (RSD) / 15648 (SCF)<br />
|<ul><li>SCF files: LimbBlastema/LB_SCF.gz</li><li>RSD files: LimbBlastema/LB_RSD.gz</li></ul><br />
|Akira Tazaki<br />
|<br />
|-<br />
|NeuraTube<br />
|Neural tube library<br />
|Neural tube<br />
|4896 (RSD) / 7905 (SCF)<br />
|<ul><li>SCF files: NeuralTube/NT_SCF.gz</li><li>RSD files: NeuralTube/NT_RSD.gz</li></ul><br />
|Akira Tazaki<br />
|<br />
|}<br />
<br />
=== Roche/454 ===<br />
The data can be found under <b>//biodata/groups/axolotl-transcriptome/raw/454</b>.<br />
{| class="wikitable"<br />
!style="width: 200px" | Name<br />
!style="width: 300px" | Description<br />
!style="width: 200px" | Tissue<br />
!style="width: 200px" | Reads<br />
!style="width: 200px" | Format<br />
!style="width: 300px" | Location<br />
!style="width: 100px" | Author<br />
!style="width: 300px" | Remarks<br />
|-<br />
|454<br />
|Mixed 454<br />
|Mixed<br />
|1,208,954<br />
|Fasta/Qual<br />
|Ax_454.tar.gz<br />
|n/a<br />
|}<br />
<br />
== Microarrays ==<br />
The data can be found under <b>//biodata/groups/crtd_tanaka/LabData/Microarrays</b>. Also consult the file <b>Contents.txt</b> in the experiment directory for more details. The raw data (*.tiff) files can be found in the subdirectory <b>Raw</b> in the experiment directory.<br />
{| class="wikitable"<br />
!style="width: 200px" | Name<br />
!style="width: 300px" | Description<br />
!style="width: 300px" | Timepoints<br />
!style="width: 200px" | Tissue<br />
!style="width: 110px" | Array type<br />
!style="width: 250px" | Location<br />
!style="width: 100px" | Author<br />
!style="width: 300px" | Remarks<br />
|-<br />
|Fin vs bulk<br />
|Timecourse microarray experiment using fin and bulk tissue<br />
|0, 1d, 3d<br />
|Mature tail: fin and bulk<br />
|Agilent, 44000<br />
|Fin_vs_bulk<br />
|Eugeniu Nacu<br />
|<br />
|-<br />
|Tail timecourse<br />
|Timecourse microarray experiment using tail<br />
|0, 3h, 6h, 12h, 18h, 24h, 36h, 48h, 72h, 120h, 168h, 288h<br />
|Mature tail<br />
|Agilent, 44000<br />
|Tail_timecourse<br />
|Eugeniu Nacu<br />
|<br />
|-<br />
|Limb timecourse<br />
|Timecourse microarray experiment using limb<br />
|0, 3h, 6h, 9h, 12h, 24h, 36h, 52h, 72h, 120h, 168h, 288h, 528h<br />
|Mature limb and limb bud<br />
|Agilent, 44000<br />
|Limb_timecourse<br />
|Dunja Knapp<br />
|<br />
|}</div>
Serghein
https://wiki.tanakalab.org/index.php?title=Datasets&diff=274
Datasets
2013-06-30T16:33:04Z
<p>Serghein: /* Roche/454 */</p>
<hr />
<div>== Sequences ==<br />
=== Illumina ===<br />
The data can be found under <b>//biodata/groups/axolotl-transcriptome/raw/Illumina</b>.<br />
{| class="wikitable sortable"<br />
!style="width: 200px" class="unsortable" | Name<br />
!style="width: 300px" class="unsortable" | Description<br />
!style="width: 200px" | Tissue<br />
!style="width: 90px" class="unsortable" | Type<br />
!style="width: 80px" class="unsortable" | Read length<br />
!style="width: 100px" class="unsortable"| Fragment size<br />
!style="width: 150px" | Reads<br />
!style="width: 100px" class="unsortable" | Format<br />
!style="width: 200px" class="unsortable" | Location<br />
!style="width: 100px" | Author<br />
!style="width: 300px" class="unsortable" | Remarks<br />
|-<br />
|Mature spinal cord<br />
|Mature axolotl spinal cord<br />
|Spinal cord<br />
|Paired-ended<br />
|100bp<br />
|200-250bp<br />
|65,753,941<br />
|FastQ<br />
|SpinalCord/mSC.fastq.tar.gz<br />
|Akira Tazaki<br />
|<br />
|- <br />
|Injured spinal cord<br />
|Injured axolotl spinal cord, 6dpi<br />
|Spinal cord<br />
|Paired-ended<br />
|100bp<br />
|200-250bp<br />
|78,459,950<br />
|FastQ<br />
|SpinalCord/6diSC.fastq.tar.gz<br />
|Akira Tazaki<br />
|<br />
|-<br />
|Mature spinal cord<br />
|Mature axolotl spinal cord, replicate 2, crossing 142x5<br />
|Spinal cord<br />
|Paired-ended<br />
|100bp<br />
|180bp<br />
|101,769,559<br />
|FastQ<br />
|SpinalCord/mSC_142x5.fastq.tar.gz<br />
|Akira Tazaki<br />
|Due to a sequencer failure only the first 66 bases are safe<br />
|- <br />
|Mature spinal cord<br />
|Mature axolotl spinal cord, replicate 3, crossing 96x6<br />
|Spinal cord<br />
|Paired-ended<br />
|100bp<br />
|180bp<br />
|95,946,545<br />
|FastQ<br />
|SpinalCord/mSC_96x6.fastq.tar.gz<br />
|Akira Tazaki<br />
|Due to a sequencer failure only the first 66 bases are safe<br />
|- <br />
|Injured spinal cord<br />
|Injured axolotl spinal cord, 6dpi, replicate 2, crossing 142x5<br />
|Spinal cord<br />
|Paired-ended<br />
|100bp<br />
|180bp<br />
|96,626,387<br />
|FastQ<br />
|SpinalCord/6diSC_142x5.fastq.tar.gz<br />
|Akira Tazaki<br />
|Due to a sequencer failure only the first 66 bases are safe<br />
|- <br />
|Injured spinal cord<br />
|Injured axolotl spinal cord, 6dpi, replicate 3, crossing 96x5<br />
|Spinal cord<br />
|Paired-ended<br />
|100bp<br />
|180bp<br />
|99,855,603<br />
|FastQ<br />
|SpinalCord/6diSC_96x5.fastq.tar.gz<br />
|Akira Tazaki<br />
|Due to a sequencer failure only the first 66 bases are safe<br />
|-<br />
|Mature limb<br />
|Mature axolotl forelimb<br />
|Limb<br />
|Single-ended<br />
|76bp<br />
|n/a<br />
|65,934,228<br />
|FastQ<br />
|Limb/Mature.fastq.tar.gz<br />
|Dunja Knapp<br />
|<br />
|-<br />
|Amputated limb (36h)<br />
|Amputated axolotl forelimb (36hpa)<br />
|Limb<br />
|Single-ended<br />
|76bp<br />
|n/a<br />
|65,250,768<br />
|FastQ<br />
|Limb/36h_amp.fastq.tar.gz<br />
|Dunja Knapp<br />
|<br />
|-<br />
|Amputated limb (72h)<br />
|Amputated axolotl forelimb (72hpa)<br />
|Limb<br />
|Single-ended<br />
|76bp<br />
|n/a<br />
|62,970,898<br />
|FastQ<br />
|Limb/72h_amp.fastq.tar.gz<br />
|Dunja Knapp<br />
|<br />
|-<br />
|Lateral wound (36h)<br />
|Injured (lateral wound) axolotl forelimb (36hpw)<br />
|Limb<br />
|Single-ended<br />
|76bp<br />
|n/a<br />
|66,361,470<br />
|FastQ<br />
|Limb/36h_lw.fastq.tar.gz<br />
|Dunja Knapp<br />
|<br />
|-<br />
|Lateral wound (72h)<br />
|Injured (lateral wound) axolotl forelimb (72hpw)<br />
|Limb<br />
|Single-ended<br />
|76bp<br />
|n/a<br />
|64,133,834<br />
|FastQ<br />
|Limb/72h_lw.fastq.tar.gz<br />
|Dunja Knapp<br />
|<br />
|-<br />
|LPM-transplant<br />
|Blastema samples of a LPM-transplanted animal: mature and 1dpa<br />
|Limb blastema<br />
|Single-ended<br />
|<br />
|180bp<br />
|<ul><li>Mature: 35,982,029</li><li>1dpa: 39,824,276</li></ul><br />
|FastQ<br />
|LPM/An3.fastq.tar.gz<br />
|Prayag Murawala/Dunja Knapp<br />
|GFP-labeled LPM was transplanted to a white-host embryo. The limb of the host was amputated and the blastema sample was collected.<br />
|-<br />
|LPM-transplant<br />
|Blastema samples of a LPM-transplanted animal: mature and 10dpa<br />
|Limb blastema<br />
|Single-ended<br />
|<br />
|180bp<br />
|<ul><li>Mature: 47,155,937</li><li>10dpa: 40,468,959</li></ul><br />
|FastQ<br />
|LPM/An4.fastq.tar.gz<br />
|Prayag Murawala/Dunja Knapp<br />
|GFP-labeled LPM was transplanted to a white-host embryo. The limb of the host was amputated and the blastema sample was collected.<br />
|-<br />
|LPM-transplant<br />
|Blastema samples of a LPM-transplanted animal: mature and 5dpa<br />
|Limb blastema<br />
|Single-ended<br />
|<br />
|180bp<br />
|<ul><li>Mature: 38,879,295</li><li>5dpa: 33,775,319</li></ul><br />
|FastQ<br />
|LPM/An6.fastq.tar.gz<br />
|Prayag Murawala/Dunja Knapp<br />
|GFP-labeled LPM was transplanted to a white-host embryo. The limb of the host was amputated and the blastema sample was collected.<br />
|-<br />
|LPM-transplant<br />
|Blastema samples of a LPM-transplanted animal: mature and 7dpa<br />
|Limb blastema<br />
|Single-ended<br />
|<br />
|180bp<br />
|<ul><li>Mature: 52,385,146</li><li>7dpa: 54,639,187</li></ul><br />
|FastQ<br />
|LPM/An7.fastq.tar.gz<br />
|Prayag Murawala/Dunja Knapp<br />
|GFP-labeled LPM was transplanted to a white-host embryo. The limb of the host was amputated and the blastema sample was collected. <br />
|-<br />
|LPM-transplant<br />
|Blastema samples of a LPM-transplanted animal: mature and 3dpa<br />
|Limb blastema<br />
|Single-ended<br />
|<br />
|180bp<br />
|<ul><li>Mature: 69,327,682</li><li>3dpa: 52,633,592</li></ul><br />
|FastQ<br />
|LPM/An8.fastq.tar.gz<br />
|Prayag Murawala/Dunja Knapp<br />
|GFP-labeled LPM was transplanted to a white-host embryo. The limb of the host was amputated and the blastema sample was collected.<br />
|}<br />
<br />
Unsorted Illumina data can be found under <b>//biodata/groups/crtd_tanaka/LabData/Sequencing/Illumina/unsorted</b>.<br /><br />
For some of the data sets quality check was performed using FastQC. The statistics can be found under <b>//biodata/groups/crtd_tanaka/LabData/Sequencing/Illumina/qualitycheck</b>.<br />
<br />
=== Sanger ===<br />
The data can be found under <b>//biodata/groups/axolotl-transcriptome/raw/Sanger</b>.<br />
{| class="wikitable sortable"<br />
!style="width: 200px" class="unsortable" | Name<br />
!style="width: 300px" class="unsortable" | Description<br />
!style="width: 200px" | Tissue<br />
!style="width: 200px" | Sequences<br />
!style="width: 300px" class="unsortable" | Location<br />
!style="width: 100px" | Author<br />
!style="width: 300px" class="unsortable" | Remarks<br />
|-<br />
|LimbBlastema<br />
|Limb blastema library<br />
|Limb blastema<br />
|20160 (RSD) / 15648 (SCF)<br />
|<ul><li>SCF files: LimbBlastema/LB_SCF.gz</li><li>RSD files: LimbBlastema/LB_RSD.gz</li></ul><br />
|Akira Tazaki<br />
|<br />
|-<br />
|NeuraTube<br />
|Neural tube library<br />
|Teural tube<br />
|4896 (RSD) / 7905 (SCF)<br />
|<ul><li>SCF files: NeuralTube/NT_SCF.gz</li><li>RSD files: NeuralTube/NT_RSD.gz</li></ul><br />
|Akira Tazaki<br />
|<br />
|}<br />
<br />
=== Roche/454 ===<br />
The data can be found under <b>//biodata/groups/axolotl-transcriptome/raw/454</b>.<br />
{| class="wikitable"<br />
!style="width: 200px" | Name<br />
!style="width: 300px" | Description<br />
!style="width: 200px" | Tissue<br />
!style="width: 200px" | Reads<br />
!style="width: 200px" | Format<br />
!style="width: 300px" | Location<br />
!style="width: 100px" | Author<br />
!style="width: 300px" | Remarks<br />
|-<br />
|454<br />
|Mixed 454<br />
|Mixed<br />
|1,208,954<br />
|Fasta/Qual<br />
|Ax_454.tar.gz<br />
|n/a<br />
|}<br />
<br />
== Microarrays ==<br />
The data can be found under <b>//biodata/groups/crtd_tanaka/LabData/Microarrays</b>. Also consult the file <b>Contents.txt</b> in the experiment directory for more details. The raw data (*.tiff) files can be found in the subdirectory <b>Raw</b> in the experiment directory.<br />
{| class="wikitable"<br />
!style="width: 200px" | Name<br />
!style="width: 300px" | Description<br />
!style="width: 300px" | Timepoints<br />
!style="width: 200px" | Tissue<br />
!style="width: 110px" | Array type<br />
!style="width: 250px" | Location<br />
!style="width: 100px" | Author<br />
!style="width: 300px" | Remarks<br />
|-<br />
|Fin vs bulk<br />
|Timecourse microarray experiment using fin and bulk tissue<br />
|0, 1d, 3d<br />
|Mature tail: fin and bulk<br />
|Agilent, 44000<br />
|Fin_vs_bulk<br />
|Eugeniu Nacu<br />
|<br />
|-<br />
|Tail timecourse<br />
|Timecourse microarray experiment using tail<br />
|0, 3h, 6h, 12h, 18h, 24h, 36h, 48h, 72h, 120h, 168h, 288h<br />
|Mature tail<br />
|Agilent, 44000<br />
|Tail_timecourse<br />
|Eugeniu Nacu<br />
|<br />
|-<br />
|Limb timecourse<br />
|Timecourse microarray experiment using limb<br />
|0, 3h, 6h, 9h, 12h, 24h, 36h, 52h, 72h, 120h, 168h, 288h, 528h<br />
|Mature limb and limb bud<br />
|Agilent, 44000<br />
|Limb_timecourse<br />
|Dunja Knapp<br />
|<br />
|}</div>
Serghein
https://wiki.tanakalab.org/index.php?title=Datasets&diff=273
Datasets
2013-06-30T16:32:52Z
<p>Serghein: /* Sanger */</p>
<hr />
<div>== Sequences ==<br />
=== Illumina ===<br />
The data can be found under <b>//biodata/groups/axolotl-transcriptome/raw/Illumina</b>.<br />
{| class="wikitable sortable"<br />
!style="width: 200px" class="unsortable" | Name<br />
!style="width: 300px" class="unsortable" | Description<br />
!style="width: 200px" | Tissue<br />
!style="width: 90px" class="unsortable" | Type<br />
!style="width: 80px" class="unsortable" | Read length<br />
!style="width: 100px" class="unsortable"| Fragment size<br />
!style="width: 150px" | Reads<br />
!style="width: 100px" class="unsortable" | Format<br />
!style="width: 200px" class="unsortable" | Location<br />
!style="width: 100px" | Author<br />
!style="width: 300px" class="unsortable" | Remarks<br />
|-<br />
|Mature spinal cord<br />
|Mature axolotl spinal cord<br />
|Spinal cord<br />
|Paired-ended<br />
|100bp<br />
|200-250bp<br />
|65,753,941<br />
|FastQ<br />
|SpinalCord/mSC.fastq.tar.gz<br />
|Akira Tazaki<br />
|<br />
|- <br />
|Injured spinal cord<br />
|Injured axolotl spinal cord, 6dpi<br />
|Spinal cord<br />
|Paired-ended<br />
|100bp<br />
|200-250bp<br />
|78,459,950<br />
|FastQ<br />
|SpinalCord/6diSC.fastq.tar.gz<br />
|Akira Tazaki<br />
|<br />
|-<br />
|Mature spinal cord<br />
|Mature axolotl spinal cord, replicate 2, crossing 142x5<br />
|Spinal cord<br />
|Paired-ended<br />
|100bp<br />
|180bp<br />
|101,769,559<br />
|FastQ<br />
|SpinalCord/mSC_142x5.fastq.tar.gz<br />
|Akira Tazaki<br />
|Due to a sequencer failure only the first 66 bases are safe<br />
|- <br />
|Mature spinal cord<br />
|Mature axolotl spinal cord, replicate 3, crossing 96x6<br />
|Spinal cord<br />
|Paired-ended<br />
|100bp<br />
|180bp<br />
|95,946,545<br />
|FastQ<br />
|SpinalCord/mSC_96x6.fastq.tar.gz<br />
|Akira Tazaki<br />
|Due to a sequencer failure only the first 66 bases are safe<br />
|- <br />
|Injured spinal cord<br />
|Injured axolotl spinal cord, 6dpi, replicate 2, crossing 142x5<br />
|Spinal cord<br />
|Paired-ended<br />
|100bp<br />
|180bp<br />
|96,626,387<br />
|FastQ<br />
|SpinalCord/6diSC_142x5.fastq.tar.gz<br />
|Akira Tazaki<br />
|Due to a sequencer failure only the first 66 bases are safe<br />
|- <br />
|Injured spinal cord<br />
|Injured axolotl spinal cord, 6dpi, replicate 3, crossing 96x5<br />
|Spinal cord<br />
|Paired-ended<br />
|100bp<br />
|180bp<br />
|99,855,603<br />
|FastQ<br />
|SpinalCord/6diSC_96x5.fastq.tar.gz<br />
|Akira Tazaki<br />
|Due to a sequencer failure only the first 66 bases are safe<br />
|-<br />
|Mature limb<br />
|Mature axolotl forelimb<br />
|Limb<br />
|Single-ended<br />
|76bp<br />
|n/a<br />
|65,934,228<br />
|FastQ<br />
|Limb/Mature.fastq.tar.gz<br />
|Dunja Knapp<br />
|<br />
|-<br />
|Amputated limb (36h)<br />
|Amputated axolotl forelimb (36hpa)<br />
|Limb<br />
|Single-ended<br />
|76bp<br />
|n/a<br />
|65,250,768<br />
|FastQ<br />
|Limb/36h_amp.fastq.tar.gz<br />
|Dunja Knapp<br />
|<br />
|-<br />
|Amputated limb (72h)<br />
|Amputated axolotl forelimb (72hpa)<br />
|Limb<br />
|Single-ended<br />
|76bp<br />
|n/a<br />
|62,970,898<br />
|FastQ<br />
|Limb/72h_amp.fastq.tar.gz<br />
|Dunja Knapp<br />
|<br />
|-<br />
|Lateral wound (36h)<br />
|Injured (lateral wound) axolotl forelimb (36hpw)<br />
|Limb<br />
|Single-ended<br />
|76bp<br />
|n/a<br />
|66,361,470<br />
|FastQ<br />
|Limb/36h_lw.fastq.tar.gz<br />
|Dunja Knapp<br />
|<br />
|-<br />
|Lateral wound (72h)<br />
|Injured (lateral wound) axolotl forelimb (72hpw)<br />
|Limb<br />
|Single-ended<br />
|76bp<br />
|n/a<br />
|64,133,834<br />
|FastQ<br />
|Limb/72h_lw.fastq.tar.gz<br />
|Dunja Knapp<br />
|<br />
|-<br />
|LPM-transplant<br />
|Blastema samples of a LPM-transplanted animal: mature and 1dpa<br />
|Limb blastema<br />
|Single-ended<br />
|<br />
|180bp<br />
|<ul><li>Mature: 35,982,029</li><li>1dpa: 39,824,276</li></ul><br />
|FastQ<br />
|LPM/An3.fastq.tar.gz<br />
|Prayag Murawala/Dunja Knapp<br />
|GFP-labeled LPM was transplanted to a white-host embryo. The limb of the host was amputated and the blastema sample was collected.<br />
|-<br />
|LPM-transplant<br />
|Blastema samples of a LPM-transplanted animal: mature and 10dpa<br />
|Limb blastema<br />
|Single-ended<br />
|<br />
|180bp<br />
|<ul><li>Mature: 47,155,937</li><li>10dpa: 40,468,959</li></ul><br />
|FastQ<br />
|LPM/An4.fastq.tar.gz<br />
|Prayag Murawala/Dunja Knapp<br />
|GFP-labeled LPM was transplanted to a white-host embryo. The limb of the host was amputated and the blastema sample was collected.<br />
|-<br />
|LPM-transplant<br />
|Blastema samples of a LPM-transplanted animal: mature and 5dpa<br />
|Limb blastema<br />
|Single-ended<br />
|<br />
|180bp<br />
|<ul><li>Mature: 38,879,295</li><li>5dpa: 33,775,319</li></ul><br />
|FastQ<br />
|LPM/An6.fastq.tar.gz<br />
|Prayag Murawala/Dunja Knapp<br />
|GFP-labeled LPM was transplanted to a white-host embryo. The limb of the host was amputated and the blastema sample was collected.<br />
|-<br />
|LPM-transplant<br />
|Blastema samples of a LPM-transplanted animal: mature and 7dpa<br />
|Limb blastema<br />
|Single-ended<br />
|<br />
|180bp<br />
|<ul><li>Mature: 52,385,146</li><li>7dpa: 54,639,187</li></ul><br />
|FastQ<br />
|LPM/An7.fastq.tar.gz<br />
|Prayag Murawala/Dunja Knapp<br />
|GFP-labeled LPM was transplanted to a white-host embryo. The limb of the host was amputated and the blastema sample was collected. <br />
|-<br />
|LPM-transplant<br />
|Blastema samples of a LPM-transplanted animal: mature and 3dpa<br />
|Limb blastema<br />
|Single-ended<br />
|<br />
|180bp<br />
|<ul><li>Mature: 69,327,682</li><li>3dpa: 52,633,592</li></ul><br />
|FastQ<br />
|LPM/An8.fastq.tar.gz<br />
|Prayag Murawala/Dunja Knapp<br />
|GFP-labeled LPM was transplanted to a white-host embryo. The limb of the host was amputated and the blastema sample was collected.<br />
|}<br />
<br />
Unsorted Illumina data can be found under <b>//biodata/groups/crtd_tanaka/LabData/Sequencing/Illumina/unsorted</b>.<br /><br />
For some of the data sets quality check was performed using FastQC. The statistics can be found under <b>//biodata/groups/crtd_tanaka/LabData/Sequencing/Illumina/qualitycheck</b>.<br />
<br />
=== Sanger ===<br />
The data can be found under <b>//biodata/groups/axolotl-transcriptome/raw/Sanger</b>.<br />
{| class="wikitable sortable"<br />
!style="width: 200px" class="unsortable" | Name<br />
!style="width: 300px" class="unsortable" | Description<br />
!style="width: 200px" | Tissue<br />
!style="width: 200px" | Sequences<br />
!style="width: 300px" class="unsortable" | Location<br />
!style="width: 100px" | Author<br />
!style="width: 300px" class="unsortable" | Remarks<br />
|-<br />
|LimbBlastema<br />
|Limb blastema library<br />
|Limb blastema<br />
|20160 (RSD) / 15648 (SCF)<br />
|<ul><li>SCF files: LimbBlastema/LB_SCF.gz</li><li>RSD files: LimbBlastema/LB_RSD.gz</li></ul><br />
|Akira Tazaki<br />
|<br />
|-<br />
|NeuraTube<br />
|Neural tube library<br />
|Teural tube<br />
|4896 (RSD) / 7905 (SCF)<br />
|<ul><li>SCF files: NeuralTube/NT_SCF.gz</li><li>RSD files: NeuralTube/NT_RSD.gz</li></ul><br />
|Akira Tazaki<br />
|<br />
|}<br />
<br />
=== Roche/454 ===<br />
The data can be found under <b>//biodata/groups/crtd_tanaka/LabData/Sequencing/454</b>.<br />
{| class="wikitable"<br />
!style="width: 200px" | Name<br />
!style="width: 300px" | Description<br />
!style="width: 200px" | Tissue<br />
!style="width: 200px" | Reads<br />
!style="width: 200px" | Format<br />
!style="width: 300px" | Location<br />
!style="width: 100px" | Author<br />
!style="width: 300px" | Remarks<br />
|-<br />
|454<br />
|Mixed 454<br />
|Mixed<br />
|1,208,954<br />
|Fasta/Qual<br />
|Ax_454.tar.gz<br />
|n/a<br />
|}<br />
<br />
== Microarrays ==<br />
The data can be found under <b>//biodata/groups/crtd_tanaka/LabData/Microarrays</b>. Also consult the file <b>Contents.txt</b> in the experiment directory for more details. The raw data (*.tiff) files can be found in the subdirectory <b>Raw</b> in the experiment directory.<br />
{| class="wikitable"<br />
!style="width: 200px" | Name<br />
!style="width: 300px" | Description<br />
!style="width: 300px" | Timepoints<br />
!style="width: 200px" | Tissue<br />
!style="width: 110px" | Array type<br />
!style="width: 250px" | Location<br />
!style="width: 100px" | Author<br />
!style="width: 300px" | Remarks<br />
|-<br />
|Fin vs bulk<br />
|Timecourse microarray experiment using fin and bulk tissue<br />
|0, 1d, 3d<br />
|Mature tail: fin and bulk<br />
|Agilent, 44000<br />
|Fin_vs_bulk<br />
|Eugeniu Nacu<br />
|<br />
|-<br />
|Tail timecourse<br />
|Timecourse microarray experiment using tail<br />
|0, 3h, 6h, 12h, 18h, 24h, 36h, 48h, 72h, 120h, 168h, 288h<br />
|Mature tail<br />
|Agilent, 44000<br />
|Tail_timecourse<br />
|Eugeniu Nacu<br />
|<br />
|-<br />
|Limb timecourse<br />
|Timecourse microarray experiment using limb<br />
|0, 3h, 6h, 9h, 12h, 24h, 36h, 52h, 72h, 120h, 168h, 288h, 528h<br />
|Mature limb and limb bud<br />
|Agilent, 44000<br />
|Limb_timecourse<br />
|Dunja Knapp<br />
|<br />
|}</div>
Serghein
https://wiki.tanakalab.org/index.php?title=Datasets&diff=272
Datasets
2013-06-30T16:32:03Z
<p>Serghein: /* Illumina */</p>
<hr />
<div>== Sequences ==<br />
=== Illumina ===<br />
The data can be found under <b>//biodata/groups/axolotl-transcriptome/raw/Illumina</b>.<br />
{| class="wikitable sortable"<br />
!style="width: 200px" class="unsortable" | Name<br />
!style="width: 300px" class="unsortable" | Description<br />
!style="width: 200px" | Tissue<br />
!style="width: 90px" class="unsortable" | Type<br />
!style="width: 80px" class="unsortable" | Read length<br />
!style="width: 100px" class="unsortable"| Fragment size<br />
!style="width: 150px" | Reads<br />
!style="width: 100px" class="unsortable" | Format<br />
!style="width: 200px" class="unsortable" | Location<br />
!style="width: 100px" | Author<br />
!style="width: 300px" class="unsortable" | Remarks<br />
|-<br />
|Mature spinal cord<br />
|Mature axolotl spinal cord<br />
|Spinal cord<br />
|Paired-ended<br />
|100bp<br />
|200-250bp<br />
|65,753,941<br />
|FastQ<br />
|SpinalCord/mSC.fastq.tar.gz<br />
|Akira Tazaki<br />
|<br />
|- <br />
|Injured spinal cord<br />
|Injured axolotl spinal cord, 6dpi<br />
|Spinal cord<br />
|Paired-ended<br />
|100bp<br />
|200-250bp<br />
|78,459,950<br />
|FastQ<br />
|SpinalCord/6diSC.fastq.tar.gz<br />
|Akira Tazaki<br />
|<br />
|-<br />
|Mature spinal cord<br />
|Mature axolotl spinal cord, replicate 2, crossing 142x5<br />
|Spinal cord<br />
|Paired-ended<br />
|100bp<br />
|180bp<br />
|101,769,559<br />
|FastQ<br />
|SpinalCord/mSC_142x5.fastq.tar.gz<br />
|Akira Tazaki<br />
|Due to a sequencer failure only the first 66 bases are safe<br />
|- <br />
|Mature spinal cord<br />
|Mature axolotl spinal cord, replicate 3, crossing 96x6<br />
|Spinal cord<br />
|Paired-ended<br />
|100bp<br />
|180bp<br />
|95,946,545<br />
|FastQ<br />
|SpinalCord/mSC_96x6.fastq.tar.gz<br />
|Akira Tazaki<br />
|Due to a sequencer failure only the first 66 bases are safe<br />
|- <br />
|Injured spinal cord<br />
|Injured axolotl spinal cord, 6dpi, replicate 2, crossing 142x5<br />
|Spinal cord<br />
|Paired-ended<br />
|100bp<br />
|180bp<br />
|96,626,387<br />
|FastQ<br />
|SpinalCord/6diSC_142x5.fastq.tar.gz<br />
|Akira Tazaki<br />
|Due to a sequencer failure only the first 66 bases are safe<br />
|- <br />
|Injured spinal cord<br />
|Injured axolotl spinal cord, 6dpi, replicate 3, crossing 96x5<br />
|Spinal cord<br />
|Paired-ended<br />
|100bp<br />
|180bp<br />
|99,855,603<br />
|FastQ<br />
|SpinalCord/6diSC_96x5.fastq.tar.gz<br />
|Akira Tazaki<br />
|Due to a sequencer failure only the first 66 bases are safe<br />
|-<br />
|Mature limb<br />
|Mature axolotl forelimb<br />
|Limb<br />
|Single-ended<br />
|76bp<br />
|n/a<br />
|65,934,228<br />
|FastQ<br />
|Limb/Mature.fastq.tar.gz<br />
|Dunja Knapp<br />
|<br />
|-<br />
|Amputated limb (36h)<br />
|Amputated axolotl forelimb (36hpa)<br />
|Limb<br />
|Single-ended<br />
|76bp<br />
|n/a<br />
|65,250,768<br />
|FastQ<br />
|Limb/36h_amp.fastq.tar.gz<br />
|Dunja Knapp<br />
|<br />
|-<br />
|Amputated limb (72h)<br />
|Amputated axolotl forelimb (72hpa)<br />
|Limb<br />
|Single-ended<br />
|76bp<br />
|n/a<br />
|62,970,898<br />
|FastQ<br />
|Limb/72h_amp.fastq.tar.gz<br />
|Dunja Knapp<br />
|<br />
|-<br />
|Lateral wound (36h)<br />
|Injured (lateral wound) axolotl forelimb (36hpw)<br />
|Limb<br />
|Single-ended<br />
|76bp<br />
|n/a<br />
|66,361,470<br />
|FastQ<br />
|Limb/36h_lw.fastq.tar.gz<br />
|Dunja Knapp<br />
|<br />
|-<br />
|Lateral wound (72h)<br />
|Injured (lateral wound) axolotl forelimb (72hpw)<br />
|Limb<br />
|Single-ended<br />
|76bp<br />
|n/a<br />
|64,133,834<br />
|FastQ<br />
|Limb/72h_lw.fastq.tar.gz<br />
|Dunja Knapp<br />
|<br />
|-<br />
|LPM-transplant<br />
|Blastema samples of a LPM-transplanted animal: mature and 1dpa<br />
|Limb blastema<br />
|Single-ended<br />
|<br />
|180bp<br />
|<ul><li>Mature: 35,982,029</li><li>1dpa: 39,824,276</li></ul><br />
|FastQ<br />
|LPM/An3.fastq.tar.gz<br />
|Prayag Murawala/Dunja Knapp<br />
|GFP-labeled LPM was transplanted to a white-host embryo. The limb of the host was amputated and the blastema sample was collected.<br />
|-<br />
|LPM-transplant<br />
|Blastema samples of a LPM-transplanted animal: mature and 10dpa<br />
|Limb blastema<br />
|Single-ended<br />
|<br />
|180bp<br />
|<ul><li>Mature: 47,155,937</li><li>10dpa: 40,468,959</li></ul><br />
|FastQ<br />
|LPM/An4.fastq.tar.gz<br />
|Prayag Murawala/Dunja Knapp<br />
|GFP-labeled LPM was transplanted to a white-host embryo. The limb of the host was amputated and the blastema sample was collected.<br />
|-<br />
|LPM-transplant<br />
|Blastema samples of a LPM-transplanted animal: mature and 5dpa<br />
|Limb blastema<br />
|Single-ended<br />
|<br />
|180bp<br />
|<ul><li>Mature: 38,879,295</li><li>5dpa: 33,775,319</li></ul><br />
|FastQ<br />
|LPM/An6.fastq.tar.gz<br />
|Prayag Murawala/Dunja Knapp<br />
|GFP-labeled LPM was transplanted to a white-host embryo. The limb of the host was amputated and the blastema sample was collected.<br />
|-<br />
|LPM-transplant<br />
|Blastema samples of a LPM-transplanted animal: mature and 7dpa<br />
|Limb blastema<br />
|Single-ended<br />
|<br />
|180bp<br />
|<ul><li>Mature: 52,385,146</li><li>7dpa: 54,639,187</li></ul><br />
|FastQ<br />
|LPM/An7.fastq.tar.gz<br />
|Prayag Murawala/Dunja Knapp<br />
|GFP-labeled LPM was transplanted to a white-host embryo. The limb of the host was amputated and the blastema sample was collected. <br />
|-<br />
|LPM-transplant<br />
|Blastema samples of a LPM-transplanted animal: mature and 3dpa<br />
|Limb blastema<br />
|Single-ended<br />
|<br />
|180bp<br />
|<ul><li>Mature: 69,327,682</li><li>3dpa: 52,633,592</li></ul><br />
|FastQ<br />
|LPM/An8.fastq.tar.gz<br />
|Prayag Murawala/Dunja Knapp<br />
|GFP-labeled LPM was transplanted to a white-host embryo. The limb of the host was amputated and the blastema sample was collected.<br />
|}<br />
<br />
Unsorted Illumina data can be found under <b>//biodata/groups/crtd_tanaka/LabData/Sequencing/Illumina/unsorted</b>.<br /><br />
For some of the data sets quality check was performed using FastQC. The statistics can be found under <b>//biodata/groups/crtd_tanaka/LabData/Sequencing/Illumina/qualitycheck</b>.<br />
<br />
=== Sanger ===<br />
The data can be found under <b>//biodata/groups/crtd_tanaka/LabData/Sequencing/Sanger</b>.<br />
{| class="wikitable sortable"<br />
!style="width: 200px" class="unsortable" | Name<br />
!style="width: 300px" class="unsortable" | Description<br />
!style="width: 200px" | Tissue<br />
!style="width: 200px" | Sequences<br />
!style="width: 300px" class="unsortable" | Location<br />
!style="width: 100px" | Author<br />
!style="width: 300px" class="unsortable" | Remarks<br />
|-<br />
|LimbBlastema<br />
|Limb blastema library<br />
|Limb blastema<br />
|20160 (RSD) / 15648 (SCF)<br />
|<ul><li>SCF files: LimbBlastema/LB_SCF.gz</li><li>RSD files: LimbBlastema/LB_RSD.gz</li></ul><br />
|Akira Tazaki<br />
|<br />
|-<br />
|NeuraTube<br />
|Neural tube library<br />
|Teural tube<br />
|4896 (RSD) / 7905 (SCF)<br />
|<ul><li>SCF files: NeuralTube/NT_SCF.gz</li><li>RSD files: NeuralTube/NT_RSD.gz</li></ul><br />
|Akira Tazaki<br />
|<br />
|}<br />
<br />
=== Roche/454 ===<br />
The data can be found under <b>//biodata/groups/crtd_tanaka/LabData/Sequencing/454</b>.<br />
{| class="wikitable"<br />
!style="width: 200px" | Name<br />
!style="width: 300px" | Description<br />
!style="width: 200px" | Tissue<br />
!style="width: 200px" | Reads<br />
!style="width: 200px" | Format<br />
!style="width: 300px" | Location<br />
!style="width: 100px" | Author<br />
!style="width: 300px" | Remarks<br />
|-<br />
|454<br />
|Mixed 454<br />
|Mixed<br />
|1,208,954<br />
|Fasta/Qual<br />
|Ax_454.tar.gz<br />
|n/a<br />
|}<br />
<br />
== Microarrays ==<br />
The data can be found under <b>//biodata/groups/crtd_tanaka/LabData/Microarrays</b>. Also consult the file <b>Contents.txt</b> in the experiment directory for more details. The raw data (*.tiff) files can be found in the subdirectory <b>Raw</b> in the experiment directory.<br />
{| class="wikitable"<br />
!style="width: 200px" | Name<br />
!style="width: 300px" | Description<br />
!style="width: 300px" | Timepoints<br />
!style="width: 200px" | Tissue<br />
!style="width: 110px" | Array type<br />
!style="width: 250px" | Location<br />
!style="width: 100px" | Author<br />
!style="width: 300px" | Remarks<br />
|-<br />
|Fin vs bulk<br />
|Timecourse microarray experiment using fin and bulk tissue<br />
|0, 1d, 3d<br />
|Mature tail: fin and bulk<br />
|Agilent, 44000<br />
|Fin_vs_bulk<br />
|Eugeniu Nacu<br />
|<br />
|-<br />
|Tail timecourse<br />
|Timecourse microarray experiment using tail<br />
|0, 3h, 6h, 12h, 18h, 24h, 36h, 48h, 72h, 120h, 168h, 288h<br />
|Mature tail<br />
|Agilent, 44000<br />
|Tail_timecourse<br />
|Eugeniu Nacu<br />
|<br />
|-<br />
|Limb timecourse<br />
|Timecourse microarray experiment using limb<br />
|0, 3h, 6h, 9h, 12h, 24h, 36h, 52h, 72h, 120h, 168h, 288h, 528h<br />
|Mature limb and limb bud<br />
|Agilent, 44000<br />
|Limb_timecourse<br />
|Dunja Knapp<br />
|<br />
|}</div>
Serghein
https://wiki.tanakalab.org/index.php?title=Overview&diff=271
Overview
2013-06-30T16:28:26Z
<p>Serghein: /* Fileservers */</p>
<hr />
<div>== Introduction ==<br />
On the pages listed below you can find most common protocols used in the lab as well as a list of lab duties along with the names of the responsible persons. Please, contact the responsible persons if you have any question, suggestions or troubles.<br />
<br />
== Axolotl ==<br />
<br />
=== Maintainance ===<br />
In this section you will find some general information on how to [[Axolotl#Maintaining_the_axolotls|maintain]] the animals.<br />
<br />
=== Feeding ===<br />
This section will give you an overview of how to [[Axolotl#Feeding|feed]] the axolotls.<br />
<br />
=== Interesting observations ===<br />
In the following section you can find some [[Axolotl#Interesting_observations|interesting observations]] concerning the axolotl, its behavior, caveats of the transgenics and many more.<br />
<br />
== Lab duties ==<br />
<ul><br />
=== Chemicals ===<br />
<li>[[Antibiotics|Antibiotics]]</li><br />
<li>[[Benzocaine|Benzocaine]]</li><br />
<li>[[Fibronectin|Fibronectin]]</li><br />
<li>[[Gelatine|Gelatine]]</li><br />
<li>[[Liquid_nitrogen|Liquid nitrogen]]</li><br />
<li>[[Primary_antibodies|Primary antibodies]]</li><br />
<li>[[Secondary_antibodies|Secondary antibodies]]</li><br />
<li>[[Serum_immunostaining|Serum immunostaining]]</li><br />
<br />
=== Hardware ===<br />
<li>[[Autoclave|Autoclave]]</li><br />
<li>[[Cryostat|Cryostat]]</li><br />
<li>[[Dissecting_microscopes|Dissecting microscopes]]</li><br />
<li>[[Leica_confocal_microscope|Leica confocal microscope]]</li><br />
<li>[[Vacuum_pumps|Vacuum pumps]]</li><br />
<li>[[Waterbath|Waterbath]]</li><br />
<br />
=== General ===<br />
<li>[[Ordering_common_stuff|Ordering common stuff]]</li><br />
<li>[[Heat_shock_competent_cells|Heat-shock competent cells]]</li><br />
</ul><br />
<br />
<br />
== Protocols ==<br />
<ul><br />
=== Cell culture ===<br />
<li>[[Blastema_cells|Blastema cells]]</li><br />
<li>[[Baculovirus_titration|Baculovirus titration]]</li><br />
<li>[[Myoblasts_electroporation|Myoblasts electroporation]]</li><br />
<li>[[Adhesive_cell_culture|Adhesive cell culture]]</li><br />
<li>[[Electroporation_of_blastema_cells|Electroporation of blastema cells]]</li><br />
<li>[[Electroporation_of_nec|Electroporation of neural epithelia cells (axolotl spinal cord)]]</li><br />
<li>[[mESC_culture|mESC culture/Cyst formation]]</li><br />
<li>[[Neurosphere_culture|Neurosphere culture]]</li><br />
=== Histology ===<br />
<li>[[Double_Immunostaining_via_antigen_retrieval|Double Immunostaining via antigen retrieval (Sherry)]]</li><br />
=== Molecular biology ===<br />
<li>[[Metamorphosis_protocol|Metamorphosis protocol (Sherry)]]</li><br />
</ul><br />
<br />
== Booking calendars ==<br />
Since some pieces of hardware are used intensively it is necessary to book them in advance. The links to the corresponding booking calendars are listed below.<br />
<ul><br />
<li><br />
Fluorescence microscopes<br />
<ul><br />
<li>[http://www.my.calendars.net/olympusszx16 Olympus SZX 16]</li><br />
<li>[http://www.my.calendars.net/new_olympus/ New Olympus SZX 16]</li><br />
<li>[http://www.my.calendars.net/Olympus_OVK Olympus OVK]</li><br />
<li>[http://www.my.calendars.net/axio_observer/ Axio Observer]</li><br />
</ul><br />
</li><br />
<li><br />
Microinjectors and electroporators and dissecting microscope<br />
<ul><br />
<li>Room 0.232<br />
<ul> <br />
<li>[http://www.my.calendars.net/electroporator Nepa Gene]</li><br />
<li>[http://www.my.calendars.net/electroporator2 ECM 830]</li><br />
<li>[http://www.my.calendars.net/stereoscope2/d01/11/2012 Olympus dissecting microscope]</li><br />
</ul><br />
</li><br />
<li>Lab<br />
<ul><br />
<li>[http://www.my.calendars.net/OlympusLab Olympus (next to the axolotls)]</li><br />
<li>[http://www.my.calendars.net/OlympusLab2 Olympus (next to the Microtome)]</li><br />
</ul><br />
</li><br />
</ul><br />
</li><br />
<li><br />
Confocal microscopes<br />
<ul><br />
<li>[http://www.my.calendars.net/leica_lsm Leica LSM]</li><br />
</ul><br />
</li><br />
<li><br />
Cryostats<br />
<ul><br />
<li>[http://www.my.calendars.net/cryostat1 Cryostat 1]</li><br />
<li>[http://www.my.calendars.net/cryostat2 Cryostat 2]</li><br />
</ul><br />
</li><br />
<li><br />
Microtome<br />
<ul><br />
<li>[http://www.my.calendars.net/microtome Microtome]</li><br />
</ul><br />
</li><br />
<li><br />
Paraffin embedding station<br />
<ul><br />
<li>[http://www.my.calendars.net/wax_station Paraffin embedding station]</li><br />
</ul><br />
</li><br />
</ul><br />
<br />
== Transgenic lines ==<br />
<ul><br />
<li>[[Transgenic_axolotl_lines|Axolotl (A.mexicanum)]]</li><br />
<li>[[Transgenic_frog_lines|Frog (X.laevis)]]</li><br />
</ul><br />
<br />
== Digital data ==<br />
Over the years the members of the lab have produced a lot of different data: Sanger sequences, EST libraries, images and so on. <br />
Select a category from the list below in order to view or download the data.<br />
<br />
=== Fileservers ===<br />
{| class="wikitable"<br />
!style="width: 350px" | Location<br />
!style="width: 250px" | Volume size<br />
!style="width: 350px" | Description<br />
!style="width: 350px" | Access<br />
!style="width: 350px" | Location (console only)<br />
|-<br />
|//biodata/groups/<b>crtd_tanaka</b><br />
|16 TB<br />
|General purpose storage space<br />
|Entire Tanaka lab<br />
|<i>biocluster:</i> <b>/group/crtd_tanaka</b><br />
|-<br />
|//biodata/groups/<b>tanaka-ests</b><br />
|247 GB<br />
|EST sequences<br />
|Entire Tanaka lab<br />
|<i>biocluster:</i> <b>/group/tanaka-ests</b><br />
|-<br />
|//biodata/groups/<b>axolotl-transcriptome</b><br />
|500 GB<br />
|Axolotl transcriptome data<br />
|Elly, Sergej<br />
|<i>biocluster:</i> <b>/projects/axolotl-transcriptome</b><br />
|-<br />
|//biodata/groups/<b>tanaka-saori</b><br />
|878 GB<br />
|Special directory for Saori's data<br />
|Elly, Saori, Sergej<br />
|<i>biocluster:</i> <b>/group/tanaka-saori</b><br />
|}<br />
<br />
{{Tip|The path is different, when accessing the file server from the console.}}<br />
<br />
=== Literature ===<br />
<ul><br />
<li>[[Literature#Theses|Theses]]</li><br />
<li>[[Literature#Publications|Publications]]</li><br />
</ul><br />
<br />
=== Databases ===<br />
<ul><br />
<li>[http://est.age.mpg.de/axolotl/ Axolotl transcriptome] website contains the Axolotl transcriptome assemblies</li><br />
<li>[http://newtomics.mpi-bn.mpg.de/ Newt transcriptome] website contains the Newt transcriptome assembly</li><br />
<li>[http://sandberg.cmb.ki.se/redspottednewt/ Red spotted newt transcriptome] website contains the red spotted newt transcriptome assembly</li><br />
<li>[https://python-srv1.mpi-cbg.de/axolotl/cgi-bin/login.cgi Axolotl EST] database contains several ESTs and also some additional information, e.g. the position of the well with the corresponding insert in the Blastema (BL) or Neural tube (NT) library.</li><br />
<li>[http://est.age.mpg.de/ Axologle] database contains expression profiling data of Axolotl limb regeneration</li><br />
<li>[http://est.age.mpg.de/blast/blast.html Axolotl BLAST] database contains several different BLAST-able Axolotl transciptome assemblies</li><br />
</ul><br />
<br />
=== Datasets ===<br />
<ul><br />
<li>[[Datasets#Sequences|Sequences]]<br />
<ul><br />
<li>[[Datasets#Illumina|Illumina]]</li><br />
<li>[[Datasets#Sanger|Sanger]]</li><br />
<li>[[Datasets#Roche.2F454|Roche/454]]</li><br />
</ul><br />
</li><br />
<li>[[Datasets#Microarrays|Microarrays]]<br />
</ul><br />
<br />
=== Interesting links ===<br />
<ul><br />
<li>[http://www.nytimes.com/video/2013/02/27/science/100000002087758/finding-the-visible-in-the-invisible.html Visible in the invisible]: a movie introducing a new image processing ana analysis technique developed at the MIT.</li><br />
</ul><br />
<br />
== Lab life ==<br />
<ul><br />
<li>[[Lab_photos|Lab photos]]</li><br />
<li>Further pictures can be found in <b>/biodata/groups/crtd_tanaka/LabFun/</b></li><br />
<li>The recepies for Heino's farewell present can be found under <b>/biodata/groups/crtd_tanaka/LabFun/Heino's farewell present/</b></li><br />
<li>The video of the visit of the EU commissioner can be found under <b>/biodata/groups/crtd_tanaka/LabFun/</b></li><br />
</ul></div>
Serghein
https://wiki.tanakalab.org/index.php?title=Overview&diff=270
Overview
2013-06-27T15:47:54Z
<p>Serghein: /* Booking calendars */</p>
<hr />
<div>== Introduction ==<br />
On the pages listed below you can find most common protocols used in the lab as well as a list of lab duties along with the names of the responsible persons. Please, contact the responsible persons if you have any question, suggestions or troubles.<br />
<br />
== Axolotl ==<br />
<br />
=== Maintainance ===<br />
In this section you will find some general information on how to [[Axolotl#Maintaining_the_axolotls|maintain]] the animals.<br />
<br />
=== Feeding ===<br />
This section will give you an overview of how to [[Axolotl#Feeding|feed]] the axolotls.<br />
<br />
=== Interesting observations ===<br />
In the following section you can find some [[Axolotl#Interesting_observations|interesting observations]] concerning the axolotl, its behavior, caveats of the transgenics and many more.<br />
<br />
== Lab duties ==<br />
<ul><br />
=== Chemicals ===<br />
<li>[[Antibiotics|Antibiotics]]</li><br />
<li>[[Benzocaine|Benzocaine]]</li><br />
<li>[[Fibronectin|Fibronectin]]</li><br />
<li>[[Gelatine|Gelatine]]</li><br />
<li>[[Liquid_nitrogen|Liquid nitrogen]]</li><br />
<li>[[Primary_antibodies|Primary antibodies]]</li><br />
<li>[[Secondary_antibodies|Secondary antibodies]]</li><br />
<li>[[Serum_immunostaining|Serum immunostaining]]</li><br />
<br />
=== Hardware ===<br />
<li>[[Autoclave|Autoclave]]</li><br />
<li>[[Cryostat|Cryostat]]</li><br />
<li>[[Dissecting_microscopes|Dissecting microscopes]]</li><br />
<li>[[Leica_confocal_microscope|Leica confocal microscope]]</li><br />
<li>[[Vacuum_pumps|Vacuum pumps]]</li><br />
<li>[[Waterbath|Waterbath]]</li><br />
<br />
=== General ===<br />
<li>[[Ordering_common_stuff|Ordering common stuff]]</li><br />
<li>[[Heat_shock_competent_cells|Heat-shock competent cells]]</li><br />
</ul><br />
<br />
<br />
== Protocols ==<br />
<ul><br />
=== Cell culture ===<br />
<li>[[Blastema_cells|Blastema cells]]</li><br />
<li>[[Baculovirus_titration|Baculovirus titration]]</li><br />
<li>[[Myoblasts_electroporation|Myoblasts electroporation]]</li><br />
<li>[[Adhesive_cell_culture|Adhesive cell culture]]</li><br />
<li>[[Electroporation_of_blastema_cells|Electroporation of blastema cells]]</li><br />
<li>[[Electroporation_of_nec|Electroporation of neural epithelia cells (axolotl spinal cord)]]</li><br />
<li>[[mESC_culture|mESC culture/Cyst formation]]</li><br />
<li>[[Neurosphere_culture|Neurosphere culture]]</li><br />
=== Histology ===<br />
<li>[[Double_Immunostaining_via_antigen_retrieval|Double Immunostaining via antigen retrieval (Sherry)]]</li><br />
=== Molecular biology ===<br />
<li>[[Metamorphosis_protocol|Metamorphosis protocol (Sherry)]]</li><br />
</ul><br />
<br />
== Booking calendars ==<br />
Since some pieces of hardware are used intensively it is necessary to book them in advance. The links to the corresponding booking calendars are listed below.<br />
<ul><br />
<li><br />
Fluorescence microscopes<br />
<ul><br />
<li>[http://www.my.calendars.net/olympusszx16 Olympus SZX 16]</li><br />
<li>[http://www.my.calendars.net/new_olympus/ New Olympus SZX 16]</li><br />
<li>[http://www.my.calendars.net/Olympus_OVK Olympus OVK]</li><br />
<li>[http://www.my.calendars.net/axio_observer/ Axio Observer]</li><br />
</ul><br />
</li><br />
<li><br />
Microinjectors and electroporators and dissecting microscope<br />
<ul><br />
<li>Room 0.232<br />
<ul> <br />
<li>[http://www.my.calendars.net/electroporator Nepa Gene]</li><br />
<li>[http://www.my.calendars.net/electroporator2 ECM 830]</li><br />
<li>[http://www.my.calendars.net/stereoscope2/d01/11/2012 Olympus dissecting microscope]</li><br />
</ul><br />
</li><br />
<li>Lab<br />
<ul><br />
<li>[http://www.my.calendars.net/OlympusLab Olympus (next to the axolotls)]</li><br />
<li>[http://www.my.calendars.net/OlympusLab2 Olympus (next to the Microtome)]</li><br />
</ul><br />
</li><br />
</ul><br />
</li><br />
<li><br />
Confocal microscopes<br />
<ul><br />
<li>[http://www.my.calendars.net/leica_lsm Leica LSM]</li><br />
</ul><br />
</li><br />
<li><br />
Cryostats<br />
<ul><br />
<li>[http://www.my.calendars.net/cryostat1 Cryostat 1]</li><br />
<li>[http://www.my.calendars.net/cryostat2 Cryostat 2]</li><br />
</ul><br />
</li><br />
<li><br />
Microtome<br />
<ul><br />
<li>[http://www.my.calendars.net/microtome Microtome]</li><br />
</ul><br />
</li><br />
<li><br />
Paraffin embedding station<br />
<ul><br />
<li>[http://www.my.calendars.net/wax_station Paraffin embedding station]</li><br />
</ul><br />
</li><br />
</ul><br />
<br />
== Transgenic lines ==<br />
<ul><br />
<li>[[Transgenic_axolotl_lines|Axolotl (A.mexicanum)]]</li><br />
<li>[[Transgenic_frog_lines|Frog (X.laevis)]]</li><br />
</ul><br />
<br />
== Digital data ==<br />
Over the years the members of the lab have produced a lot of different data: Sanger sequences, EST libraries, images and so on. <br />
Select a category from the list below in order to view or download the data.<br />
<br />
=== Fileservers ===<br />
{| class="wikitable"<br />
!style="width: 350px" | Location<br />
!style="width: 250px" | Volume size<br />
!style="width: 350px" | Description<br />
!style="width: 350px" | Access<br />
!style="width: 350px" | Location (console only)<br />
|-<br />
|//biodata/groups/<b>crtd_tanaka</b><br />
|16 TB<br />
|General purpose storage space<br />
|Entire Tanaka lab<br />
|<i>biocluster:</i> <b>/group/crtd_tanaka</b><br />
|-<br />
|//biodata/groups/<b>tanaka-ests</b><br />
|247 GB<br />
|EST sequences<br />
|Entire Tanaka lab<br />
|<i>biocluster:</i> <b>/group/tanaka-ests</b><br />
|-<br />
|//biodata/groups/<b>axolotl-transcriptome</b><br />
|117 GB<br />
|Axolotl transcriptome data<br />
|Elly, Sergej<br />
|<i>biocluster:</i> <b>/projects/axolotl-transcriptome</b><br />
|-<br />
|//biodata/groups/<b>tanaka-saori</b><br />
|878 GB<br />
|Special directory for Saori's data<br />
|Elly, Saori, Sergej<br />
|<i>biocluster:</i> <b>/group/tanaka-saori</b><br />
|}<br />
<br />
{{Tip|The path is different, when accessing the file server from the console.}}<br />
<br />
=== Literature ===<br />
<ul><br />
<li>[[Literature#Theses|Theses]]</li><br />
<li>[[Literature#Publications|Publications]]</li><br />
</ul><br />
<br />
=== Databases ===<br />
<ul><br />
<li>[http://est.age.mpg.de/axolotl/ Axolotl transcriptome] website contains the Axolotl transcriptome assemblies</li><br />
<li>[http://newtomics.mpi-bn.mpg.de/ Newt transcriptome] website contains the Newt transcriptome assembly</li><br />
<li>[http://sandberg.cmb.ki.se/redspottednewt/ Red spotted newt transcriptome] website contains the red spotted newt transcriptome assembly</li><br />
<li>[https://python-srv1.mpi-cbg.de/axolotl/cgi-bin/login.cgi Axolotl EST] database contains several ESTs and also some additional information, e.g. the position of the well with the corresponding insert in the Blastema (BL) or Neural tube (NT) library.</li><br />
<li>[http://est.age.mpg.de/ Axologle] database contains expression profiling data of Axolotl limb regeneration</li><br />
<li>[http://est.age.mpg.de/blast/blast.html Axolotl BLAST] database contains several different BLAST-able Axolotl transciptome assemblies</li><br />
</ul><br />
<br />
=== Datasets ===<br />
<ul><br />
<li>[[Datasets#Sequences|Sequences]]<br />
<ul><br />
<li>[[Datasets#Illumina|Illumina]]</li><br />
<li>[[Datasets#Sanger|Sanger]]</li><br />
<li>[[Datasets#Roche.2F454|Roche/454]]</li><br />
</ul><br />
</li><br />
<li>[[Datasets#Microarrays|Microarrays]]<br />
</ul><br />
<br />
=== Interesting links ===<br />
<ul><br />
<li>[http://www.nytimes.com/video/2013/02/27/science/100000002087758/finding-the-visible-in-the-invisible.html Visible in the invisible]: a movie introducing a new image processing ana analysis technique developed at the MIT.</li><br />
</ul><br />
<br />
== Lab life ==<br />
<ul><br />
<li>[[Lab_photos|Lab photos]]</li><br />
<li>Further pictures can be found in <b>/biodata/groups/crtd_tanaka/LabFun/</b></li><br />
<li>The recepies for Heino's farewell present can be found under <b>/biodata/groups/crtd_tanaka/LabFun/Heino's farewell present/</b></li><br />
<li>The video of the visit of the EU commissioner can be found under <b>/biodata/groups/crtd_tanaka/LabFun/</b></li><br />
</ul></div>
Serghein
https://wiki.tanakalab.org/index.php?title=Overview&diff=269
Overview
2013-06-19T09:16:07Z
<p>Serghein: /* Databases */</p>
<hr />
<div>== Introduction ==<br />
On the pages listed below you can find most common protocols used in the lab as well as a list of lab duties along with the names of the responsible persons. Please, contact the responsible persons if you have any question, suggestions or troubles.<br />
<br />
== Axolotl ==<br />
<br />
=== Maintainance ===<br />
In this section you will find some general information on how to [[Axolotl#Maintaining_the_axolotls|maintain]] the animals.<br />
<br />
=== Feeding ===<br />
This section will give you an overview of how to [[Axolotl#Feeding|feed]] the axolotls.<br />
<br />
=== Interesting observations ===<br />
In the following section you can find some [[Axolotl#Interesting_observations|interesting observations]] concerning the axolotl, its behavior, caveats of the transgenics and many more.<br />
<br />
== Lab duties ==<br />
<ul><br />
=== Chemicals ===<br />
<li>[[Antibiotics|Antibiotics]]</li><br />
<li>[[Benzocaine|Benzocaine]]</li><br />
<li>[[Fibronectin|Fibronectin]]</li><br />
<li>[[Gelatine|Gelatine]]</li><br />
<li>[[Liquid_nitrogen|Liquid nitrogen]]</li><br />
<li>[[Primary_antibodies|Primary antibodies]]</li><br />
<li>[[Secondary_antibodies|Secondary antibodies]]</li><br />
<li>[[Serum_immunostaining|Serum immunostaining]]</li><br />
<br />
=== Hardware ===<br />
<li>[[Autoclave|Autoclave]]</li><br />
<li>[[Cryostat|Cryostat]]</li><br />
<li>[[Dissecting_microscopes|Dissecting microscopes]]</li><br />
<li>[[Leica_confocal_microscope|Leica confocal microscope]]</li><br />
<li>[[Vacuum_pumps|Vacuum pumps]]</li><br />
<li>[[Waterbath|Waterbath]]</li><br />
<br />
=== General ===<br />
<li>[[Ordering_common_stuff|Ordering common stuff]]</li><br />
<li>[[Heat_shock_competent_cells|Heat-shock competent cells]]</li><br />
</ul><br />
<br />
<br />
== Protocols ==<br />
<ul><br />
=== Cell culture ===<br />
<li>[[Blastema_cells|Blastema cells]]</li><br />
<li>[[Baculovirus_titration|Baculovirus titration]]</li><br />
<li>[[Myoblasts_electroporation|Myoblasts electroporation]]</li><br />
<li>[[Adhesive_cell_culture|Adhesive cell culture]]</li><br />
<li>[[Electroporation_of_blastema_cells|Electroporation of blastema cells]]</li><br />
<li>[[Electroporation_of_nec|Electroporation of neural epithelia cells (axolotl spinal cord)]]</li><br />
<li>[[mESC_culture|mESC culture/Cyst formation]]</li><br />
<li>[[Neurosphere_culture|Neurosphere culture]]</li><br />
=== Histology ===<br />
<li>[[Double_Immunostaining_via_antigen_retrieval|Double Immunostaining via antigen retrieval (Sherry)]]</li><br />
=== Molecular biology ===<br />
<li>[[Metamorphosis_protocol|Metamorphosis protocol (Sherry)]]</li><br />
</ul><br />
<br />
== Booking calendars ==<br />
Since some pieces of hardware are used intensively it is necessary to book them in advance. The links to the corresponding booking calendars are listed below.<br />
<ul><br />
<li><br />
Fluorescence microscopes<br />
<ul><br />
<li>[http://www.my.calendars.net/olympusszx16 Olympus SZX 16]</li><br />
<li>[http://www.my.calendars.net/new_olympus/ New Olympus SZX 16]</li><br />
<li>[http://www.my.calendars.net/Olympus_OVK Olympus OVK]</li><br />
<li>[http://www.my.calendars.net/axio_observer/ Axio Observer]</li><br />
</ul><br />
</li><br />
<li><br />
Microinjectors and electroporators and dissecting microscope<br />
<ul><br />
<li>Room 0.232<br />
<ul> <br />
<li>[http://www.my.calendars.net/electroporator Nepa Gene]</li><br />
<li>[http://www.my.calendars.net/electroporator2 ECM 830]</li><br />
<li>[http://www.my.calendars.net/stereoscope2/d01/11/2012 Olympus dissecting microscope]</li><br />
</ul><br />
</li><br />
<li>Lab<br />
<ul><br />
<li>[http://www.my.calendars.net/OlympusLab Olympus (next to the axolotls)]</li><br />
<li>[http://www.my.calendars.net/OlympusLab2 Olympus (next to the Microtome)]</li><br />
</ul><br />
</li><br />
</ul><br />
</li><br />
<li><br />
Confocal microscopes<br />
<ul><br />
<li>[http://www.my.calendars.net/leica_lsm Leica LSM]</li><br />
</ul><br />
</li><br />
<li><br />
Cryostats<br />
<ul><br />
<li>[http://www.my.calendars.net/cryostat1 Cryostat 1]</li><br />
<li>[http://www.my.calendars.net/cryostat2 Cryostat 2]</li><br />
</ul><br />
</li><br />
<li><br />
Microtome<br />
<ul><br />
<li>[http://www.my.calendars.net/microtome Microtome]</li><br />
</ul><br />
</li><br />
</ul><br />
<br />
== Transgenic lines ==<br />
<ul><br />
<li>[[Transgenic_axolotl_lines|Axolotl (A.mexicanum)]]</li><br />
<li>[[Transgenic_frog_lines|Frog (X.laevis)]]</li><br />
</ul><br />
<br />
== Digital data ==<br />
Over the years the members of the lab have produced a lot of different data: Sanger sequences, EST libraries, images and so on. <br />
Select a category from the list below in order to view or download the data.<br />
<br />
=== Fileservers ===<br />
{| class="wikitable"<br />
!style="width: 350px" | Location<br />
!style="width: 250px" | Volume size<br />
!style="width: 350px" | Description<br />
!style="width: 350px" | Access<br />
!style="width: 350px" | Location (console only)<br />
|-<br />
|//biodata/groups/<b>crtd_tanaka</b><br />
|16 TB<br />
|General purpose storage space<br />
|Entire Tanaka lab<br />
|<i>biocluster:</i> <b>/group/crtd_tanaka</b><br />
|-<br />
|//biodata/groups/<b>tanaka-ests</b><br />
|247 GB<br />
|EST sequences<br />
|Entire Tanaka lab<br />
|<i>biocluster:</i> <b>/group/tanaka-ests</b><br />
|-<br />
|//biodata/groups/<b>axolotl-transcriptome</b><br />
|117 GB<br />
|Axolotl transcriptome data<br />
|Elly, Sergej<br />
|<i>biocluster:</i> <b>/projects/axolotl-transcriptome</b><br />
|-<br />
|//biodata/groups/<b>tanaka-saori</b><br />
|878 GB<br />
|Special directory for Saori's data<br />
|Elly, Saori, Sergej<br />
|<i>biocluster:</i> <b>/group/tanaka-saori</b><br />
|}<br />
<br />
{{Tip|The path is different, when accessing the file server from the console.}}<br />
<br />
=== Literature ===<br />
<ul><br />
<li>[[Literature#Theses|Theses]]</li><br />
<li>[[Literature#Publications|Publications]]</li><br />
</ul><br />
<br />
=== Databases ===<br />
<ul><br />
<li>[http://est.age.mpg.de/axolotl/ Axolotl transcriptome] website contains the Axolotl transcriptome assemblies</li><br />
<li>[http://newtomics.mpi-bn.mpg.de/ Newt transcriptome] website contains the Newt transcriptome assembly</li><br />
<li>[http://sandberg.cmb.ki.se/redspottednewt/ Red spotted newt transcriptome] website contains the red spotted newt transcriptome assembly</li><br />
<li>[https://python-srv1.mpi-cbg.de/axolotl/cgi-bin/login.cgi Axolotl EST] database contains several ESTs and also some additional information, e.g. the position of the well with the corresponding insert in the Blastema (BL) or Neural tube (NT) library.</li><br />
<li>[http://est.age.mpg.de/ Axologle] database contains expression profiling data of Axolotl limb regeneration</li><br />
<li>[http://est.age.mpg.de/blast/blast.html Axolotl BLAST] database contains several different BLAST-able Axolotl transciptome assemblies</li><br />
</ul><br />
<br />
=== Datasets ===<br />
<ul><br />
<li>[[Datasets#Sequences|Sequences]]<br />
<ul><br />
<li>[[Datasets#Illumina|Illumina]]</li><br />
<li>[[Datasets#Sanger|Sanger]]</li><br />
<li>[[Datasets#Roche.2F454|Roche/454]]</li><br />
</ul><br />
</li><br />
<li>[[Datasets#Microarrays|Microarrays]]<br />
</ul><br />
<br />
=== Interesting links ===<br />
<ul><br />
<li>[http://www.nytimes.com/video/2013/02/27/science/100000002087758/finding-the-visible-in-the-invisible.html Visible in the invisible]: a movie introducing a new image processing ana analysis technique developed at the MIT.</li><br />
</ul><br />
<br />
== Lab life ==<br />
<ul><br />
<li>[[Lab_photos|Lab photos]]</li><br />
<li>Further pictures can be found in <b>/biodata/groups/crtd_tanaka/LabFun/</b></li><br />
<li>The recepies for Heino's farewell present can be found under <b>/biodata/groups/crtd_tanaka/LabFun/Heino's farewell present/</b></li><br />
<li>The video of the visit of the EU commissioner can be found under <b>/biodata/groups/crtd_tanaka/LabFun/</b></li><br />
</ul></div>
Serghein
https://wiki.tanakalab.org/index.php?title=Overview&diff=268
Overview
2013-06-19T09:13:52Z
<p>Serghein: /* Databases */</p>
<hr />
<div>== Introduction ==<br />
On the pages listed below you can find most common protocols used in the lab as well as a list of lab duties along with the names of the responsible persons. Please, contact the responsible persons if you have any question, suggestions or troubles.<br />
<br />
== Axolotl ==<br />
<br />
=== Maintainance ===<br />
In this section you will find some general information on how to [[Axolotl#Maintaining_the_axolotls|maintain]] the animals.<br />
<br />
=== Feeding ===<br />
This section will give you an overview of how to [[Axolotl#Feeding|feed]] the axolotls.<br />
<br />
=== Interesting observations ===<br />
In the following section you can find some [[Axolotl#Interesting_observations|interesting observations]] concerning the axolotl, its behavior, caveats of the transgenics and many more.<br />
<br />
== Lab duties ==<br />
<ul><br />
=== Chemicals ===<br />
<li>[[Antibiotics|Antibiotics]]</li><br />
<li>[[Benzocaine|Benzocaine]]</li><br />
<li>[[Fibronectin|Fibronectin]]</li><br />
<li>[[Gelatine|Gelatine]]</li><br />
<li>[[Liquid_nitrogen|Liquid nitrogen]]</li><br />
<li>[[Primary_antibodies|Primary antibodies]]</li><br />
<li>[[Secondary_antibodies|Secondary antibodies]]</li><br />
<li>[[Serum_immunostaining|Serum immunostaining]]</li><br />
<br />
=== Hardware ===<br />
<li>[[Autoclave|Autoclave]]</li><br />
<li>[[Cryostat|Cryostat]]</li><br />
<li>[[Dissecting_microscopes|Dissecting microscopes]]</li><br />
<li>[[Leica_confocal_microscope|Leica confocal microscope]]</li><br />
<li>[[Vacuum_pumps|Vacuum pumps]]</li><br />
<li>[[Waterbath|Waterbath]]</li><br />
<br />
=== General ===<br />
<li>[[Ordering_common_stuff|Ordering common stuff]]</li><br />
<li>[[Heat_shock_competent_cells|Heat-shock competent cells]]</li><br />
</ul><br />
<br />
<br />
== Protocols ==<br />
<ul><br />
=== Cell culture ===<br />
<li>[[Blastema_cells|Blastema cells]]</li><br />
<li>[[Baculovirus_titration|Baculovirus titration]]</li><br />
<li>[[Myoblasts_electroporation|Myoblasts electroporation]]</li><br />
<li>[[Adhesive_cell_culture|Adhesive cell culture]]</li><br />
<li>[[Electroporation_of_blastema_cells|Electroporation of blastema cells]]</li><br />
<li>[[Electroporation_of_nec|Electroporation of neural epithelia cells (axolotl spinal cord)]]</li><br />
<li>[[mESC_culture|mESC culture/Cyst formation]]</li><br />
<li>[[Neurosphere_culture|Neurosphere culture]]</li><br />
=== Histology ===<br />
<li>[[Double_Immunostaining_via_antigen_retrieval|Double Immunostaining via antigen retrieval (Sherry)]]</li><br />
=== Molecular biology ===<br />
<li>[[Metamorphosis_protocol|Metamorphosis protocol (Sherry)]]</li><br />
</ul><br />
<br />
== Booking calendars ==<br />
Since some pieces of hardware are used intensively it is necessary to book them in advance. The links to the corresponding booking calendars are listed below.<br />
<ul><br />
<li><br />
Fluorescence microscopes<br />
<ul><br />
<li>[http://www.my.calendars.net/olympusszx16 Olympus SZX 16]</li><br />
<li>[http://www.my.calendars.net/new_olympus/ New Olympus SZX 16]</li><br />
<li>[http://www.my.calendars.net/Olympus_OVK Olympus OVK]</li><br />
<li>[http://www.my.calendars.net/axio_observer/ Axio Observer]</li><br />
</ul><br />
</li><br />
<li><br />
Microinjectors and electroporators and dissecting microscope<br />
<ul><br />
<li>Room 0.232<br />
<ul> <br />
<li>[http://www.my.calendars.net/electroporator Nepa Gene]</li><br />
<li>[http://www.my.calendars.net/electroporator2 ECM 830]</li><br />
<li>[http://www.my.calendars.net/stereoscope2/d01/11/2012 Olympus dissecting microscope]</li><br />
</ul><br />
</li><br />
<li>Lab<br />
<ul><br />
<li>[http://www.my.calendars.net/OlympusLab Olympus (next to the axolotls)]</li><br />
<li>[http://www.my.calendars.net/OlympusLab2 Olympus (next to the Microtome)]</li><br />
</ul><br />
</li><br />
</ul><br />
</li><br />
<li><br />
Confocal microscopes<br />
<ul><br />
<li>[http://www.my.calendars.net/leica_lsm Leica LSM]</li><br />
</ul><br />
</li><br />
<li><br />
Cryostats<br />
<ul><br />
<li>[http://www.my.calendars.net/cryostat1 Cryostat 1]</li><br />
<li>[http://www.my.calendars.net/cryostat2 Cryostat 2]</li><br />
</ul><br />
</li><br />
<li><br />
Microtome<br />
<ul><br />
<li>[http://www.my.calendars.net/microtome Microtome]</li><br />
</ul><br />
</li><br />
</ul><br />
<br />
== Transgenic lines ==<br />
<ul><br />
<li>[[Transgenic_axolotl_lines|Axolotl (A.mexicanum)]]</li><br />
<li>[[Transgenic_frog_lines|Frog (X.laevis)]]</li><br />
</ul><br />
<br />
== Digital data ==<br />
Over the years the members of the lab have produced a lot of different data: Sanger sequences, EST libraries, images and so on. <br />
Select a category from the list below in order to view or download the data.<br />
<br />
=== Fileservers ===<br />
{| class="wikitable"<br />
!style="width: 350px" | Location<br />
!style="width: 250px" | Volume size<br />
!style="width: 350px" | Description<br />
!style="width: 350px" | Access<br />
!style="width: 350px" | Location (console only)<br />
|-<br />
|//biodata/groups/<b>crtd_tanaka</b><br />
|16 TB<br />
|General purpose storage space<br />
|Entire Tanaka lab<br />
|<i>biocluster:</i> <b>/group/crtd_tanaka</b><br />
|-<br />
|//biodata/groups/<b>tanaka-ests</b><br />
|247 GB<br />
|EST sequences<br />
|Entire Tanaka lab<br />
|<i>biocluster:</i> <b>/group/tanaka-ests</b><br />
|-<br />
|//biodata/groups/<b>axolotl-transcriptome</b><br />
|117 GB<br />
|Axolotl transcriptome data<br />
|Elly, Sergej<br />
|<i>biocluster:</i> <b>/projects/axolotl-transcriptome</b><br />
|-<br />
|//biodata/groups/<b>tanaka-saori</b><br />
|878 GB<br />
|Special directory for Saori's data<br />
|Elly, Saori, Sergej<br />
|<i>biocluster:</i> <b>/group/tanaka-saori</b><br />
|}<br />
<br />
{{Tip|The path is different, when accessing the file server from the console.}}<br />
<br />
=== Literature ===<br />
<ul><br />
<li>[[Literature#Theses|Theses]]</li><br />
<li>[[Literature#Publications|Publications]]</li><br />
</ul><br />
<br />
=== Databases ===<br />
<ul><br />
<li>[http://est.age.mpg.de/axolotl/ Axolotl transcriptome] website contains the Axolotl transcriptome assemblies</li><br />
<li>[http://newtomics.mpi-bn.mpg.de/ Newt transcriptome] website contains the Newt transcriptome assembly</li><br />
<li>[http://sandberg.cmb.ki.se/redspottednewt/ Red spotted newt transcriptome] website contains the red spotted newt transcriptome assembly</li><br />
<li>[https://python-srv1.mpi-cbg.de/axolotl/cgi-bin/login.cgi Axolotl EST] database contains several ESTs and also some additional information, e.g. the position of the well with the corresponding insert in the Blastema (BL) or Neural tube (NT) library.</li><br />
<li>[http://est.age.mpg.de/cgi-bin/result.py Axologle] database contains several different Axolotl transciptome assemblies</li><br />
</ul><br />
<br />
=== Datasets ===<br />
<ul><br />
<li>[[Datasets#Sequences|Sequences]]<br />
<ul><br />
<li>[[Datasets#Illumina|Illumina]]</li><br />
<li>[[Datasets#Sanger|Sanger]]</li><br />
<li>[[Datasets#Roche.2F454|Roche/454]]</li><br />
</ul><br />
</li><br />
<li>[[Datasets#Microarrays|Microarrays]]<br />
</ul><br />
<br />
=== Interesting links ===<br />
<ul><br />
<li>[http://www.nytimes.com/video/2013/02/27/science/100000002087758/finding-the-visible-in-the-invisible.html Visible in the invisible]: a movie introducing a new image processing ana analysis technique developed at the MIT.</li><br />
</ul><br />
<br />
== Lab life ==<br />
<ul><br />
<li>[[Lab_photos|Lab photos]]</li><br />
<li>Further pictures can be found in <b>/biodata/groups/crtd_tanaka/LabFun/</b></li><br />
<li>The recepies for Heino's farewell present can be found under <b>/biodata/groups/crtd_tanaka/LabFun/Heino's farewell present/</b></li><br />
<li>The video of the visit of the EU commissioner can be found under <b>/biodata/groups/crtd_tanaka/LabFun/</b></li><br />
</ul></div>
Serghein
https://wiki.tanakalab.org/index.php?title=Overview&diff=267
Overview
2013-04-29T18:27:11Z
<p>Serghein: /* Databases */</p>
<hr />
<div>== Introduction ==<br />
On the pages listed below you can find most common protocols used in the lab as well as a list of lab duties along with the names of the responsible persons. Please, contact the responsible persons if you have any question, suggestions or troubles.<br />
<br />
== Axolotl ==<br />
<br />
=== Maintainance ===<br />
In this section you will find some general information on how to [[Axolotl#Maintaining_the_axolotls|maintain]] the animals.<br />
<br />
=== Feeding ===<br />
This section will give you an overview of how to [[Axolotl#Feeding|feed]] the axolotls.<br />
<br />
=== Interesting observations ===<br />
In the following section you can find some [[Axolotl#Interesting_observations|interesting observations]] concerning the axolotl, its behavior, caveats of the transgenics and many more.<br />
<br />
== Lab duties ==<br />
<ul><br />
=== Chemicals ===<br />
<li>[[Antibiotics|Antibiotics]]</li><br />
<li>[[Benzocaine|Benzocaine]]</li><br />
<li>[[Fibronectin|Fibronectin]]</li><br />
<li>[[Gelatine|Gelatine]]</li><br />
<li>[[Liquid_nitrogen|Liquid nitrogen]]</li><br />
<li>[[Primary_antibodies|Primary antibodies]]</li><br />
<li>[[Secondary_antibodies|Secondary antibodies]]</li><br />
<li>[[Serum_immunostaining|Serum immunostaining]]</li><br />
<br />
=== Hardware ===<br />
<li>[[Autoclave|Autoclave]]</li><br />
<li>[[Cryostat|Cryostat]]</li><br />
<li>[[Dissecting_microscopes|Dissecting microscopes]]</li><br />
<li>[[Leica_confocal_microscope|Leica confocal microscope]]</li><br />
<li>[[Vacuum_pumps|Vacuum pumps]]</li><br />
<li>[[Waterbath|Waterbath]]</li><br />
<br />
=== General ===<br />
<li>[[Ordering_common_stuff|Ordering common stuff]]</li><br />
<li>[[Heat_shock_competent_cells|Heat-shock competent cells]]</li><br />
</ul><br />
<br />
<br />
== Protocols ==<br />
<ul><br />
=== Cell culture ===<br />
<li>[[Blastema_cells|Blastema cells]]</li><br />
<li>[[Baculovirus_titration|Baculovirus titration]]</li><br />
<li>[[Myoblasts_electroporation|Myoblasts electroporation]]</li><br />
<li>[[Adhesive_cell_culture|Adhesive cell culture]]</li><br />
<li>[[Electroporation_of_blastema_cells|Electroporation of blastema cells]]</li><br />
<li>[[Electroporation_of_nec|Electroporation of neural epithelia cells (axolotl spinal cord)]]</li><br />
<li>[[mESC_culture|mESC culture/Cyst formation]]</li><br />
<li>[[Neurosphere_culture|Neurosphere culture]]</li><br />
=== Histology ===<br />
<li>[[Double_Immunostaining_via_antigen_retrieval|Double Immunostaining via antigen retrieval (Sherry)]]</li><br />
=== Molecular biology ===<br />
<li>[[Metamorphosis_protocol|Metamorphosis protocol (Sherry)]]</li><br />
</ul><br />
<br />
== Booking calendars ==<br />
Since some pieces of hardware are used intensively it is necessary to book them in advance. The links to the corresponding booking calendars are listed below.<br />
<ul><br />
<li><br />
Fluorescence microscopes<br />
<ul><br />
<li>[http://www.my.calendars.net/olympusszx16 Olympus SZX 16]</li><br />
<li>[http://www.my.calendars.net/new_olympus/ New Olympus SZX 16]</li><br />
<li>[http://www.my.calendars.net/Olympus_OVK Olympus OVK]</li><br />
<li>[http://www.my.calendars.net/axio_observer/ Axio Observer]</li><br />
</ul><br />
</li><br />
<li><br />
Microinjectors and electroporators and dissecting microscope<br />
<ul><br />
<li>Room 0.232<br />
<ul> <br />
<li>[http://www.my.calendars.net/electroporator Nepa Gene]</li><br />
<li>[http://www.my.calendars.net/electroporator2 ECM 830]</li><br />
<li>[http://www.my.calendars.net/stereoscope2/d01/11/2012 Olympus dissecting microscope]</li><br />
</ul><br />
</li><br />
<li>Lab<br />
<ul><br />
<li>[http://www.my.calendars.net/OlympusLab Olympus (next to the axolotls)]</li><br />
<li>[http://www.my.calendars.net/OlympusLab2 Olympus (next to the Microtome)]</li><br />
</ul><br />
</li><br />
</ul><br />
</li><br />
<li><br />
Confocal microscopes<br />
<ul><br />
<li>[http://www.my.calendars.net/leica_lsm Leica LSM]</li><br />
</ul><br />
</li><br />
<li><br />
Cryostats<br />
<ul><br />
<li>[http://www.my.calendars.net/cryostat1 Cryostat 1]</li><br />
<li>[http://www.my.calendars.net/cryostat2 Cryostat 2]</li><br />
</ul><br />
</li><br />
<li><br />
Microtome<br />
<ul><br />
<li>[http://www.my.calendars.net/microtome Microtome]</li><br />
</ul><br />
</li><br />
</ul><br />
<br />
== Transgenic lines ==<br />
<ul><br />
<li>[[Transgenic_axolotl_lines|Axolotl (A.mexicanum)]]</li><br />
<li>[[Transgenic_frog_lines|Frog (X.laevis)]]</li><br />
</ul><br />
<br />
== Digital data ==<br />
Over the years the members of the lab have produced a lot of different data: Sanger sequences, EST libraries, images and so on. <br />
Select a category from the list below in order to view or download the data.<br />
<br />
=== Fileservers ===<br />
{| class="wikitable"<br />
!style="width: 350px" | Location<br />
!style="width: 250px" | Volume size<br />
!style="width: 350px" | Description<br />
!style="width: 350px" | Access<br />
!style="width: 350px" | Location (console only)<br />
|-<br />
|//biodata/groups/<b>crtd_tanaka</b><br />
|16 TB<br />
|General purpose storage space<br />
|Entire Tanaka lab<br />
|<i>biocluster:</i> <b>/group/crtd_tanaka</b><br />
|-<br />
|//biodata/groups/<b>tanaka-ests</b><br />
|247 GB<br />
|EST sequences<br />
|Entire Tanaka lab<br />
|<i>biocluster:</i> <b>/group/tanaka-ests</b><br />
|-<br />
|//biodata/groups/<b>axolotl-transcriptome</b><br />
|117 GB<br />
|Axolotl transcriptome data<br />
|Elly, Sergej<br />
|<i>biocluster:</i> <b>/projects/axolotl-transcriptome</b><br />
|-<br />
|//biodata/groups/<b>tanaka-saori</b><br />
|878 GB<br />
|Special directory for Saori's data<br />
|Elly, Saori, Sergej<br />
|<i>biocluster:</i> <b>/group/tanaka-saori</b><br />
|}<br />
<br />
{{Tip|The path is different, when accessing the file server from the console.}}<br />
<br />
=== Literature ===<br />
<ul><br />
<li>[[Literature#Theses|Theses]]</li><br />
<li>[[Literature#Publications|Publications]]</li><br />
</ul><br />
<br />
=== Databases ===<br />
<ul><br />
<li>[http://est.age.mpg.de/axolotl2/ Axolotl transcriptome] website contains the Axolotl transcriptome assemblies</li><br />
<li>[http://newtomics.mpi-bn.mpg.de/ Newt transcriptome] website contains the Newt transcriptome assembly</li><br />
<li>[http://sandberg.cmb.ki.se/redspottednewt/ Red spotted newt transcriptome] website contains the red spotted newt transcriptome assembly</li><br />
<li>[https://python-srv1.mpi-cbg.de/axolotl/cgi-bin/login.cgi Axolotl EST] database contains several ESTs and also some additional information, e.g. the position of the well with the corresponding insert in the Blastema (BL) or Neural tube (NT) library.</li><br />
<li>[http://est.age.mpg.de/cgi-bin/result.py Axologle] database contains several different Axolotl transciptome assemblies</li><br />
</ul><br />
<br />
=== Datasets ===<br />
<ul><br />
<li>[[Datasets#Sequences|Sequences]]<br />
<ul><br />
<li>[[Datasets#Illumina|Illumina]]</li><br />
<li>[[Datasets#Sanger|Sanger]]</li><br />
<li>[[Datasets#Roche.2F454|Roche/454]]</li><br />
</ul><br />
</li><br />
<li>[[Datasets#Microarrays|Microarrays]]<br />
</ul><br />
<br />
=== Interesting links ===<br />
<ul><br />
<li>[http://www.nytimes.com/video/2013/02/27/science/100000002087758/finding-the-visible-in-the-invisible.html Visible in the invisible]: a movie introducing a new image processing ana analysis technique developed at the MIT.</li><br />
</ul><br />
<br />
== Lab life ==<br />
<ul><br />
<li>[[Lab_photos|Lab photos]]</li><br />
<li>Further pictures can be found in <b>/biodata/groups/crtd_tanaka/LabFun/</b></li><br />
<li>The recepies for Heino's farewell present can be found under <b>/biodata/groups/crtd_tanaka/LabFun/Heino's farewell present/</b></li><br />
<li>The video of the visit of the EU commissioner can be found under <b>/biodata/groups/crtd_tanaka/LabFun/</b></li><br />
</ul></div>
Serghein
https://wiki.tanakalab.org/index.php?title=Axolotl&diff=265
Axolotl
2013-03-19T21:56:31Z
<p>Serghein: /* Interesting observations */</p>
<hr />
<div>== Maintaining the axolotls ==<br />
== Feeding ==<br />
=== Artemia (Brine shrimp eggs) ===<br />
Brine shrimp eggs are metabolically inactive and can remain in total stasis for two years while in dry oxygen-free conditions, even at temperatures below freezing. This characteristic is called cryptobiosis meaning "hidden life" (also called diapause). While in cryptobiosis, brine shrimp eggs can survive temperatures of liquid air (−190 °C or −310.0 °F) and a small percentage can survive above boiling temperature (105 °C or 221 °F) for up to two hours. <br />
<br />
Once placed in brine (salt) water, the cyst-like eggs hatch within a few hours. The nauplii, or larvae, are less than 0.5 mm in length when they first hatch. Brine shrimp have a biological life cycle of one year, during which they grow to a mature length of around one centimeter on average. This short life span, along with other characteristics such as their ability to remain dormant for long periods, has made them invaluable in scientific research, including space experiments. This ability has also enabled the use of a hybrid of brine shrimp, bred to grow larger and live longer, as Sea-Monkeys.<br />
<br />
=== Artemia Hatching Preparation: Protocol for 15 Ltr. ===<br />
Switch on the bubbler. <br/ ><br />
Take the warm water from the tap and fill it into the container, meanwhile add 325 ml volume of salt (Red Sea Coral pro Salt), when the 15 Ltr. container is filled up the salt should be dissolved already. <br/ ><br />
Switch on the heating. And make sure that the light on the top is on ☺<br />
Add 50-60 ml full of dried artemia (Stored at 40C) to this.<br />
<br />
=== Hatching preparation ===<br />
* The following protocol is considered for 15 l solution.<br />
* Switch on the bubbler.<br />
* Take the warm water from the tap and fill it into the container, meanwhile add 325 ml volume of salt (Red Sea Coral pro Salt), when the 15 Ltr. container is filled up the salt should be dissolved already.<br />
* Switch on the heating. And make sure that the light on the top is on.<br />
* Add 50-60 ml full of dried artemia (Stored at 40C) to this.<br />
<br />
Keep it like this for 2 days with aeration. And >200 Lux of light.<br /><br />
Usually they hatch within few hours but It is good to keep for 2 days to achieve a good hatching.<br /><br />
During these two days temperature can be 18°-20°C.<br /><br />
Make sure hatching container is not getting clogged during these two days.<br /><br />
<br />
== Interesting observations ==<br />
Below you can find the list of observations along with the name of the person who did the observation.<br />
<br />
{| class="wikitable sortable"<br />
!style="width: 200px" | Person<br />
!style="width: 500px" class="unsortable" | Description<br />
!style="width: 50px" | Date<br />
<br />
|}</div>
Serghein
https://wiki.tanakalab.org/index.php?title=Axolotl&diff=264
Axolotl
2013-03-19T21:37:25Z
<p>Serghein: </p>
<hr />
<div>== Maintaining the axolotls ==<br />
== Feeding ==<br />
=== Artemia (Brine shrimp eggs) ===<br />
Brine shrimp eggs are metabolically inactive and can remain in total stasis for two years while in dry oxygen-free conditions, even at temperatures below freezing. This characteristic is called cryptobiosis meaning "hidden life" (also called diapause). While in cryptobiosis, brine shrimp eggs can survive temperatures of liquid air (−190 °C or −310.0 °F) and a small percentage can survive above boiling temperature (105 °C or 221 °F) for up to two hours. <br />
<br />
Once placed in brine (salt) water, the cyst-like eggs hatch within a few hours. The nauplii, or larvae, are less than 0.5 mm in length when they first hatch. Brine shrimp have a biological life cycle of one year, during which they grow to a mature length of around one centimeter on average. This short life span, along with other characteristics such as their ability to remain dormant for long periods, has made them invaluable in scientific research, including space experiments. This ability has also enabled the use of a hybrid of brine shrimp, bred to grow larger and live longer, as Sea-Monkeys.<br />
<br />
=== Artemia Hatching Preparation: Protocol for 15 Ltr. ===<br />
Switch on the bubbler. <br/ ><br />
Take the warm water from the tap and fill it into the container, meanwhile add 325 ml volume of salt (Red Sea Coral pro Salt), when the 15 Ltr. container is filled up the salt should be dissolved already. <br/ ><br />
Switch on the heating. And make sure that the light on the top is on ☺<br />
Add 50-60 ml full of dried artemia (Stored at 40C) to this.<br />
<br />
=== Hatching preparation ===<br />
* The following protocol is considered for 15 l solution.<br />
* Switch on the bubbler.<br />
* Take the warm water from the tap and fill it into the container, meanwhile add 325 ml volume of salt (Red Sea Coral pro Salt), when the 15 Ltr. container is filled up the salt should be dissolved already.<br />
* Switch on the heating. And make sure that the light on the top is on.<br />
* Add 50-60 ml full of dried artemia (Stored at 40C) to this.<br />
<br />
Keep it like this for 2 days with aeration. And >200 Lux of light.<br /><br />
Usually they hatch within few hours but It is good to keep for 2 days to achieve a good hatching.<br /><br />
During these two days temperature can be 18°-20°C.<br /><br />
Make sure hatching container is not getting clogged during these two days.<br /><br />
<br />
== Interesting observations ==<br />
Below you can find the list of observations along with the name of the person who did the observation.<br />
<br />
{| class="wikitable sortable"<br />
!style="width: 200px" | Person<br />
!style="width: 500px" class="unsortable" | Description<br />
!style="width: 50px" | Date<br />
|-<br />
|Prayag Murawala, Dunja Knapp<br />
|Axolotl epidermis moves continuously from the shoulder to the finger tips.<br />
|19.02.2013<br />
|}</div>
Serghein
https://wiki.tanakalab.org/index.php?title=Overview&diff=263
Overview
2013-03-19T21:33:06Z
<p>Serghein: /* Axolotl */</p>
<hr />
<div>== Introduction ==<br />
On the pages listed below you can find most common protocols used in the lab as well as a list of lab duties along with the names of the responsible persons. Please, contact the responsible persons if you have any question, suggestions or troubles.<br />
<br />
== Axolotl ==<br />
<br />
=== Maintainance ===<br />
In this section you will find some general information on how to [[Axolotl#Maintaining_the_axolotls|maintain]] the animals.<br />
<br />
=== Feeding ===<br />
This section will give you an overview of how to [[Axolotl#Feeding|feed]] the axolotls.<br />
<br />
=== Interesting observations ===<br />
In the following section you can find some [[Axolotl#Interesting_observations|interesting observations]] conserning the axolotl, its behavior, caveats of the transgenics and many more.<br />
<br />
== Lab duties ==<br />
<ul><br />
=== Chemicals ===<br />
<li>[[Antibiotics|Antibiotics]]</li><br />
<li>[[Benzocaine|Benzocaine]]</li><br />
<li>[[Fibronectin|Fibronectin]]</li><br />
<li>[[Gelatine|Gelatine]]</li><br />
<li>[[Liquid_nitrogen|Liquid nitrogen]]</li><br />
<li>[[Primary_antibodies|Primary antibodies]]</li><br />
<li>[[Secondary_antibodies|Secondary antibodies]]</li><br />
<li>[[Serum_immunostaining|Serum immunostaining]]</li><br />
<br />
=== Hardware ===<br />
<li>[[Autoclave|Autoclave]]</li><br />
<li>[[Cryostat|Cryostat]]</li><br />
<li>[[Dissecting_microscopes|Dissecting microscopes]]</li><br />
<li>[[Leica_confocal_microscope|Leica confocal microscope]]</li><br />
<li>[[Vacuum_pumps|Vacuum pumps]]</li><br />
<li>[[Waterbath|Waterbath]]</li><br />
<br />
=== General ===<br />
<li>[[Ordering_common_stuff|Ordering common stuff]]</li><br />
<li>[[Heat_shock_competent_cells|Heat-shock competent cells]]</li><br />
</ul><br />
<br />
<br />
== Protocols ==<br />
<ul><br />
=== Cell culture ===<br />
<li>[[Blastema_cells|Blastema cells]]</li><br />
<li>[[Baculovirus_titration|Baculovirus titration]]</li><br />
<li>[[Myoblasts_electroporation|Myoblasts electroporation]]</li><br />
<li>[[Adhesive_cell_culture|Adhesive cell culture]]</li><br />
<li>[[Electroporation_of_blastema_cells|Electroporation of blastema cells]]</li><br />
<li>[[Electroporation_of_nec|Electroporation of neural epithelia cells (axolotl spinal cord)]]</li><br />
<li>[[mESC_culture|mESC culture/Cyst formation]]</li><br />
<li>[[Neurosphere_culture|Neurosphere culture]]</li><br />
=== Histology ===<br />
<li>[[Double_Immunostaining_via_antigen_retrieval|Double Immunostaining via antigen retrieval (Sherry)]]</li><br />
=== Molecular biology ===<br />
<li>[[Metamorphosis_protocol|Metamorphosis protocol (Sherry)]]</li><br />
</ul><br />
<br />
== Booking calendars ==<br />
Since some pieces of hardware are used intensively it is necessary to book them in advance. The links to the corresponding booking calendars are listed below.<br />
<ul><br />
<li><br />
Fluorescence microscopes<br />
<ul><br />
<li>[http://www.my.calendars.net/olympusszx16 Olympus SZX 16]</li><br />
<li>[http://www.my.calendars.net/new_olympus/ New Olympus SZX 16]</li><br />
<li>[http://www.my.calendars.net/Olympus_OVK Olympus OVK]</li><br />
<li>[http://www.my.calendars.net/axio_observer/ Axio Observer]</li><br />
</ul><br />
</li><br />
<li><br />
Microinjectors and electroporators and dissecting microscope<br />
<ul><br />
<li>Room 0.232<br />
<ul> <br />
<li>[http://www.my.calendars.net/electroporator Nepa Gene]</li><br />
<li>[http://www.my.calendars.net/electroporator2 ECM 830]</li><br />
<li>[http://www.my.calendars.net/stereoscope2/d01/11/2012 Olympus dissecting microscope]</li><br />
</ul><br />
</li><br />
<li>Lab<br />
<ul><br />
<li>[http://www.my.calendars.net/OlympusLab Olympus (next to the axolotls)]</li><br />
<li>[http://www.my.calendars.net/OlympusLab2 Olympus (next to the Microtome)]</li><br />
</ul><br />
</li><br />
</ul><br />
</li><br />
<li><br />
Confocal microscopes<br />
<ul><br />
<li>[http://www.my.calendars.net/leica_lsm Leica LSM]</li><br />
</ul><br />
</li><br />
<li><br />
Cryostats<br />
<ul><br />
<li>[http://www.my.calendars.net/cryostat1 Cryostat 1]</li><br />
<li>[http://www.my.calendars.net/cryostat2 Cryostat 2]</li><br />
</ul><br />
</li><br />
<li><br />
Microtome<br />
<ul><br />
<li>[http://www.my.calendars.net/microtome Microtome]</li><br />
</ul><br />
</li><br />
</ul><br />
<br />
== Transgenic lines ==<br />
<ul><br />
<li>[[Transgenic_axolotl_lines|Axolotl (A.mexicanum)]]</li><br />
<li>[[Transgenic_frog_lines|Frog (X.laevis)]]</li><br />
</ul><br />
<br />
== Digital data ==<br />
Over the years the members of the lab have produced a lot of different data: Sanger sequences, EST libraries, images and so on. <br />
Select a category from the list below in order to view or download the data.<br />
<br />
=== Fileservers ===<br />
{| class="wikitable"<br />
!style="width: 350px" | Location<br />
!style="width: 250px" | Volume size<br />
!style="width: 350px" | Description<br />
!style="width: 350px" | Access<br />
!style="width: 350px" | Location (console only)<br />
|-<br />
|//biodata/groups/<b>crtd_tanaka</b><br />
|16 TB<br />
|General purpose storage space<br />
|Entire Tanaka lab<br />
|<i>biocluster:</i> <b>/group/crtd_tanaka</b><br />
|-<br />
|//biodata/groups/<b>tanaka-ests</b><br />
|247 GB<br />
|EST sequences<br />
|Entire Tanaka lab<br />
|<i>biocluster:</i> <b>/group/tanaka-ests</b><br />
|-<br />
|//biodata/groups/<b>axolotl-transcriptome</b><br />
|117 GB<br />
|Axolotl transcriptome data<br />
|Elly, Sergej<br />
|<i>biocluster:</i> <b>/projects/axolotl-transcriptome</b><br />
|-<br />
|//biodata/groups/<b>tanaka-saori</b><br />
|878 GB<br />
|Special directory for Saori's data<br />
|Elly, Saori, Sergej<br />
|<i>biocluster:</i> <b>/group/tanaka-saori</b><br />
|}<br />
<br />
{{Tip|The path is different, when accessing the file server from the console.}}<br />
<br />
=== Literature ===<br />
<ul><br />
<li>[[Literature#Theses|Theses]]</li><br />
<li>[[Literature#Publications|Publications]]</li><br />
</ul><br />
<br />
=== Databases ===<br />
<ul><br />
<li>[https://python-srv1.mpi-cbg.de/axolotl/cgi-bin/login.cgi Axolotl EST] database contains several ESTs and also some additional information, e.g. the position of the well with the corresponding insert in the Blastema (BL) or Neural tube (NT) library.</li><br />
<li>[http://est.age.mpg.de/cgi-bin/result.py Axologle] database contains several different Axolotl transciptome assemblies</li><br />
</ul><br />
<br />
=== Datasets ===<br />
<ul><br />
<li>[[Datasets#Sequences|Sequences]]<br />
<ul><br />
<li>[[Datasets#Illumina|Illumina]]</li><br />
<li>[[Datasets#Sanger|Sanger]]</li><br />
<li>[[Datasets#Roche.2F454|Roche/454]]</li><br />
</ul><br />
</li><br />
<li>[[Datasets#Microarrays|Microarrays]]<br />
</ul><br />
<br />
=== Interesting links ===<br />
<ul><br />
<li>[http://www.nytimes.com/video/2013/02/27/science/100000002087758/finding-the-visible-in-the-invisible.html Visible in the invisible]: a movie introducing a new image processing ana analysis technique developed at the MIT.</li><br />
</ul><br />
<br />
== Lab life ==<br />
<ul><br />
<li>[[Lab_photos|Lab photos]]</li><br />
<li>Further pictures can be found in <b>/biodata/groups/crtd_tanaka/LabFun/</b></li><br />
<li>The recepies for Heino's farewell present can be found under <b>/biodata/groups/crtd_tanaka/LabFun/Heino's farewell present/</b></li><br />
<li>The video of the visit of the EU commissioner can be found under <b>/biodata/groups/crtd_tanaka/LabFun/</b></li><br />
</ul></div>
Serghein
https://wiki.tanakalab.org/index.php?title=File:Master_Thesis_Shabanova.pdf&diff=262
File:Master Thesis Shabanova.pdf
2013-03-08T14:53:03Z
<p>Serghein: </p>
<hr />
<div></div>
Serghein
https://wiki.tanakalab.org/index.php?title=Literature&diff=261
Literature
2013-03-08T14:52:17Z
<p>Serghein: /* Theses */</p>
<hr />
<div>== Theses ==<br />
{| class="wikitable sortable"<br />
!style="width: 650px" | Title<br />
!style="width: 250px" | Author<br />
!style="width: 50px" | Year<br />
!style="width: 200px" | Type<br />
|-<br />
|[[Media:Thesis Yu Zhu.pdf|Reconstitution of three-dimensional neuroepithelia from mouse and human pluripotent stem cells]]<br />
|Yu Zhu<br />
|2012<br />
|PhD thesis<br />
|-<br />
|[[Media:Master_Thesis_Shabanova.pdf|Molecular factors required for maintenance of regeneration in the ectopic nerve-induced blastema on the anterior upper arm of the forelimb in <i>Ambystoma mexicanum</i>]]<br />
|Elena Shabanova<br />
|2012<br />
|Master's thesis<br />
|-<br />
|[[Media:Master_Thesis_Plyasunova.pdf|Making transgenic axolotl for lineage tracing of connective tissue during limb regeneration]]<br />
|Liubov Plyasunova<br />
|2012<br />
|Master's thesis<br />
|}<br />
<br />
== Publications ==<br />
{| class="wikitable sortable"<br />
!style="width: 650px" | Title<br />
!style="width: 250px" | First author<br />
!style="width: 50px" | Year<br />
!style="width: 250px" | Journal<br />
|-<br />
|[[Media:YZ_2013.pdf|3D Neuroepithelial Culture from hESCs and Its Use for Quantitative Conversion to RPE]]<br />
|Yu Zhu<br />
|2013<br />
|PLOS ONE<br />
|-<br />
|[[Media:PM_2012.pdf|Regeneration: The ultimate example of wound healing]]<br />
|Prayag Murawala<br />
|2012<br />
|Seminars in Cell & Developmental Biology<br />
|}</div>
Serghein
https://wiki.tanakalab.org/index.php?title=Overview&diff=260
Overview
2013-02-28T21:57:14Z
<p>Serghein: </p>
<hr />
<div>== Introduction ==<br />
On the pages listed below you can find most common protocols used in the lab as well as a list of lab duties along with the names of the responsible persons. Please, contact the responsible persons if you have any question, suggestions or troubles.<br />
<br />
== Axolotl ==<br />
<ul><br />
<li>[[Axolotl#Maintaining_the_axolotls|Maintainance]]</li><br />
<li>[[Axolotl#Feeding|Feeding]]</li><br />
</ul><br />
<br />
== Lab duties ==<br />
<ul><br />
=== Chemicals ===<br />
<li>[[Antibiotics|Antibiotics]]</li><br />
<li>[[Benzocaine|Benzocaine]]</li><br />
<li>[[Fibronectin|Fibronectin]]</li><br />
<li>[[Gelatine|Gelatine]]</li><br />
<li>[[Liquid_nitrogen|Liquid nitrogen]]</li><br />
<li>[[Primary_antibodies|Primary antibodies]]</li><br />
<li>[[Secondary_antibodies|Secondary antibodies]]</li><br />
<li>[[Serum_immunostaining|Serum immunostaining]]</li><br />
<br />
=== Hardware ===<br />
<li>[[Autoclave|Autoclave]]</li><br />
<li>[[Cryostat|Cryostat]]</li><br />
<li>[[Dissecting_microscopes|Dissecting microscopes]]</li><br />
<li>[[Leica_confocal_microscope|Leica confocal microscope]]</li><br />
<li>[[Vacuum_pumps|Vacuum pumps]]</li><br />
<li>[[Waterbath|Waterbath]]</li><br />
<br />
=== General ===<br />
<li>[[Ordering_common_stuff|Ordering common stuff]]</li><br />
<li>[[Heat_shock_competent_cells|Heat-shock competent cells]]</li><br />
</ul><br />
<br />
<br />
== Protocols ==<br />
<ul><br />
=== Cell culture ===<br />
<li>[[Blastema_cells|Blastema cells]]</li><br />
<li>[[Baculovirus_titration|Baculovirus titration]]</li><br />
<li>[[Myoblasts_electroporation|Myoblasts electroporation]]</li><br />
<li>[[Adhesive_cell_culture|Adhesive cell culture]]</li><br />
<li>[[Electroporation_of_blastema_cells|Electroporation of blastema cells]]</li><br />
<li>[[Electroporation_of_nec|Electroporation of neural epithelia cells (axolotl spinal cord)]]</li><br />
<li>[[mESC_culture|mESC culture/Cyst formation]]</li><br />
<li>[[Neurosphere_culture|Neurosphere culture]]</li><br />
=== Histology ===<br />
<li>[[Double_Immunostaining_via_antigen_retrieval|Double Immunostaining via antigen retrieval (Sherry)]]</li><br />
=== Molecular biology ===<br />
<li>[[Metamorphosis_protocol|Metamorphosis protocol (Sherry)]]</li><br />
</ul><br />
<br />
== Booking calendars ==<br />
Since some pieces of hardware are used intensively it is necessary to book them in advance. The links to the corresponding booking calendars are listed below.<br />
<ul><br />
<li><br />
Fluorescence microscopes<br />
<ul><br />
<li>[http://www.my.calendars.net/olympusszx16 Olympus SZX 16]</li><br />
<li>[http://www.my.calendars.net/new_olympus/ New Olympus SZX 16]</li><br />
<li>[http://www.my.calendars.net/Olympus_OVK Olympus OVK]</li><br />
<li>[http://www.my.calendars.net/axio_observer/ Axio Observer]</li><br />
</ul><br />
</li><br />
<li><br />
Microinjectors and electroporators and dissecting microscope<br />
<ul><br />
<li>Room 0.232<br />
<ul> <br />
<li>[http://www.my.calendars.net/electroporator Nepa Gene]</li><br />
<li>[http://www.my.calendars.net/electroporator2 ECM 830]</li><br />
<li>[http://www.my.calendars.net/stereoscope2/d01/11/2012 Olympus dissecting microscope]</li><br />
</ul><br />
</li><br />
<li>Lab<br />
<ul><br />
<li>[http://www.my.calendars.net/OlympusLab Olympus (next to the axolotls)]</li><br />
<li>[http://www.my.calendars.net/OlympusLab2 Olympus (next to the Microtome)]</li><br />
</ul><br />
</li><br />
</ul><br />
</li><br />
<li><br />
Confocal microscopes<br />
<ul><br />
<li>[http://www.my.calendars.net/leica_lsm Leica LSM]</li><br />
</ul><br />
</li><br />
<li><br />
Cryostats<br />
<ul><br />
<li>[http://www.my.calendars.net/cryostat1 Cryostat 1]</li><br />
<li>[http://www.my.calendars.net/cryostat2 Cryostat 2]</li><br />
</ul><br />
</li><br />
<li><br />
Microtome<br />
<ul><br />
<li>[http://www.my.calendars.net/microtome Microtome]</li><br />
</ul><br />
</li><br />
</ul><br />
<br />
== Transgenic lines ==<br />
<ul><br />
<li>[[Transgenic_axolotl_lines|Axolotl (A.mexicanum)]]</li><br />
<li>[[Transgenic_frog_lines|Frog (X.laevis)]]</li><br />
</ul><br />
<br />
== Digital data ==<br />
Over the years the members of the lab have produced a lot of different data: Sanger sequences, EST libraries, images and so on. <br />
Select a category from the list below in order to view or download the data.<br />
<br />
=== Fileservers ===<br />
{| class="wikitable"<br />
!style="width: 350px" | Location<br />
!style="width: 250px" | Volume size<br />
!style="width: 350px" | Description<br />
!style="width: 350px" | Access<br />
!style="width: 350px" | Location (console only)<br />
|-<br />
|//biodata/groups/<b>crtd_tanaka</b><br />
|16 TB<br />
|General purpose storage space<br />
|Entire Tanaka lab<br />
|<i>biocluster:</i> <b>/group/crtd_tanaka</b><br />
|-<br />
|//biodata/groups/<b>tanaka-ests</b><br />
|247 GB<br />
|EST sequences<br />
|Entire Tanaka lab<br />
|<i>biocluster:</i> <b>/group/tanaka-ests</b><br />
|-<br />
|//biodata/groups/<b>axolotl-transcriptome</b><br />
|117 GB<br />
|Axolotl transcriptome data<br />
|Elly, Sergej<br />
|<i>biocluster:</i> <b>/projects/axolotl-transcriptome</b><br />
|-<br />
|//biodata/groups/<b>tanaka-saori</b><br />
|878 GB<br />
|Special directory for Saori's data<br />
|Elly, Saori, Sergej<br />
|<i>biocluster:</i> <b>/group/tanaka-saori</b><br />
|}<br />
<br />
{{Tip|The path is different, when accessing the file server from the console.}}<br />
<br />
=== Literature ===<br />
<ul><br />
<li>[[Literature#Theses|Theses]]</li><br />
<li>[[Literature#Publications|Publications]]</li><br />
</ul><br />
<br />
=== Databases ===<br />
<ul><br />
<li>[https://python-srv1.mpi-cbg.de/axolotl/cgi-bin/login.cgi Axolotl EST] database contains several ESTs and also some additional information, e.g. the position of the well with the corresponding insert in the Blastema (BL) or Neural tube (NT) library.</li><br />
<li>[http://est.age.mpg.de/cgi-bin/result.py Axologle] database contains several different Axolotl transciptome assemblies</li><br />
</ul><br />
<br />
=== Datasets ===<br />
<ul><br />
<li>[[Datasets#Sequences|Sequences]]<br />
<ul><br />
<li>[[Datasets#Illumina|Illumina]]</li><br />
<li>[[Datasets#Sanger|Sanger]]</li><br />
<li>[[Datasets#Roche.2F454|Roche/454]]</li><br />
</ul><br />
</li><br />
<li>[[Datasets#Microarrays|Microarrays]]<br />
</ul><br />
<br />
=== Interesting links ===<br />
<ul><br />
<li>[http://www.nytimes.com/video/2013/02/27/science/100000002087758/finding-the-visible-in-the-invisible.html Visible in the invisible]: a movie introducing a new image processing ana analysis technique developed at the MIT.</li><br />
</ul><br />
<br />
== Lab life ==<br />
<ul><br />
<li>[[Lab_photos|Lab photos]]</li><br />
<li>Further pictures can be found in <b>/biodata/groups/crtd_tanaka/LabFun/</b></li><br />
<li>The recepies for Heino's farewell present can be found under <b>/biodata/groups/crtd_tanaka/LabFun/Heino's farewell present/</b></li><br />
<li>The video of the visit of the EU commissioner can be found under <b>/biodata/groups/crtd_tanaka/LabFun/</b></li><br />
</ul></div>
Serghein
https://wiki.tanakalab.org/index.php?title=Overview&diff=250
Overview
2013-02-20T14:01:15Z
<p>Serghein: /* Booking calendars */</p>
<hr />
<div>== Introduction ==<br />
On the pages listed below you can find most common protocols used in the lab as well as a list of lab duties along with the names of the responsible persons. Please, contact the responsible persons if you have any question, suggestions or troubles.<br />
<br />
== Axolotl ==<br />
<ul><br />
<li>[[Axolotl#Maintaining_the_axolotls|Maintainance]]</li><br />
<li>[[Axolotl#Feeding|Feeding]]</li><br />
</ul><br />
<br />
== Lab duties ==<br />
<ul><br />
=== Chemicals ===<br />
<li>[[Antibiotics|Antibiotics]]</li><br />
<li>[[Benzocaine|Benzocaine]]</li><br />
<li>[[Fibronectin|Fibronectin]]</li><br />
<li>[[Gelatine|Gelatine]]</li><br />
<li>[[Liquid_nitrogen|Liquid nitrogen]]</li><br />
<li>[[Primary_antibodies|Primary antibodies]]</li><br />
<li>[[Secondary_antibodies|Secondary antibodies]]</li><br />
<li>[[Serum_immunostaining|Serum immunostaining]]</li><br />
<br />
=== Hardware ===<br />
<li>[[Autoclave|Autoclave]]</li><br />
<li>[[Cryostat|Cryostat]]</li><br />
<li>[[Dissecting_microscopes|Dissecting microscopes]]</li><br />
<li>[[Leica_confocal_microscope|Leica confocal microscope]]</li><br />
<li>[[Vacuum_pumps|Vacuum pumps]]</li><br />
<li>[[Waterbath|Waterbath]]</li><br />
<br />
=== General ===<br />
<li>[[Ordering_common_stuff|Ordering common stuff]]</li><br />
<li>[[Heat_shock_competent_cells|Heat-shock competent cells]]</li><br />
</ul><br />
<br />
<br />
== Protocols ==<br />
<ul><br />
=== Cell culture ===<br />
<li>[[Blastema_cells|Blastema cells]]</li><br />
<li>[[Baculovirus_titration|Baculovirus titration]]</li><br />
<li>[[Myoblasts_electroporation|Myoblasts electroporation]]</li><br />
<li>[[Adhesive_cell_culture|Adhesive cell culture]]</li><br />
<li>[[Electroporation_of_blastema_cells|Electroporation of blastema cells]]</li><br />
<li>[[Electroporation_of_nec|Electroporation of neural epithelia cells (axolotl spinal cord)]]</li><br />
<li>[[mESC_culture|mESC culture/Cyst formation]]</li><br />
<li>[[Neurosphere_culture|Neurosphere culture]]</li><br />
=== Histology ===<br />
<li>[[Double_Immunostaining_via_antigen_retrieval|Double Immunostaining via antigen retrieval (Sherry)]]</li><br />
=== Molecular biology ===<br />
<li>[[Metamorphosis_protocol|Metamorphosis protocol (Sherry)]]</li><br />
</ul><br />
<br />
== Booking calendars ==<br />
Since some pieces of hardware are used intensively it is necessary to book them in advance. The links to the corresponding booking calendars are listed below.<br />
<ul><br />
<li><br />
Fluorescence microscopes<br />
<ul><br />
<li>[http://www.my.calendars.net/olympusszx16 Olympus SZX 16]</li><br />
<li>[http://www.my.calendars.net/new_olympus/ New Olympus SZX 16]</li><br />
<li>[http://www.my.calendars.net/Olympus_OVK Olympus OVK]</li><br />
<li>[http://www.my.calendars.net/axio_observer/ Axio Observer]</li><br />
</ul><br />
</li><br />
<li><br />
Microinjectors and electroporators and dissecting microscope<br />
<ul><br />
<li>Room 0.232<br />
<ul> <br />
<li>[http://www.my.calendars.net/electroporator Nepa Gene]</li><br />
<li>[http://www.my.calendars.net/electroporator2 ECM 830]</li><br />
<li>[http://www.my.calendars.net/stereoscope2/d01/11/2012 Olympus dissecting microscope]</li><br />
</ul><br />
</li><br />
<li>Lab<br />
<ul><br />
<li>[http://www.my.calendars.net/OlympusLab Olympus (next to the axolotls)]</li><br />
<li>[http://www.my.calendars.net/OlympusLab2 Olympus (next to the Microtome)]</li><br />
</ul><br />
</li><br />
</ul><br />
</li><br />
<li><br />
Confocal microscopes<br />
<ul><br />
<li>[http://www.my.calendars.net/leica_lsm Leica LSM]</li><br />
</ul><br />
</li><br />
<li><br />
Cryostats<br />
<ul><br />
<li>[http://www.my.calendars.net/cryostat1 Cryostat 1]</li><br />
<li>[http://www.my.calendars.net/cryostat2 Cryostat 2]</li><br />
</ul><br />
</li><br />
<li><br />
Microtome<br />
<ul><br />
<li>[http://www.my.calendars.net/microtome Microtome]</li><br />
</ul><br />
</li><br />
</ul><br />
<br />
== Transgenic lines ==<br />
<ul><br />
<li>[[Transgenic_axolotl_lines|Axolotl (A.mexicanum)]]</li><br />
<li>[[Transgenic_frog_lines|Frog (X.laevis)]]</li><br />
</ul><br />
<br />
== Digital data ==<br />
Over the years the members of the lab have produced a lot of different data: Sanger sequences, EST libraries, images and so on. <br />
Select a category from the list below in order to view or download the data.<br />
<br />
=== Fileservers ===<br />
{| class="wikitable"<br />
!style="width: 350px" | Location<br />
!style="width: 250px" | Volume size<br />
!style="width: 350px" | Description<br />
!style="width: 350px" | Access<br />
!style="width: 350px" | Location (console only)<br />
|-<br />
|//biodata/groups/<b>crtd_tanaka</b><br />
|16 TB<br />
|General purpose storage space<br />
|Entire Tanaka lab<br />
|<i>biocluster:</i> <b>/group/crtd_tanaka</b><br />
|-<br />
|//biodata/groups/<b>tanaka-ests</b><br />
|247 GB<br />
|EST sequences<br />
|Entire Tanaka lab<br />
|<i>biocluster:</i> <b>/group/tanaka-ests</b><br />
|-<br />
|//biodata/groups/<b>axolotl-transcriptome</b><br />
|117 GB<br />
|Axolotl transcriptome data<br />
|Elly, Sergej<br />
|<i>biocluster:</i> <b>/projects/axolotl-transcriptome</b><br />
|-<br />
|//biodata/groups/<b>tanaka-saori</b><br />
|878 GB<br />
|Special directory for Saori's data<br />
|Elly, Saori, Sergej<br />
|<i>biocluster:</i> <b>/group/tanaka-saori</b><br />
|}<br />
<br />
{{Tip|The path is different, when accessing the file server from the console.}}<br />
<br />
=== Literature ===<br />
<ul><br />
<li>[[Literature#Theses|Theses]]</li><br />
<li>[[Literature#Publications|Publications]]</li><br />
</ul><br />
<br />
=== Databases ===<br />
<ul><br />
<li>[https://python-srv1.mpi-cbg.de/axolotl/cgi-bin/login.cgi Axolotl EST] database contains several ESTs and also some additional information, e.g. the position of the well with the corresponding insert in the Blastema (BL) or Neural tube (NT) library.</li><br />
<li>[http://est.age.mpg.de/cgi-bin/result.py Axologle] database contains several different Axolotl transciptome assemblies</li><br />
</ul><br />
<br />
=== Datasets ===<br />
<ul><br />
<li>[[Datasets#Sequences|Sequences]]<br />
<ul><br />
<li>[[Datasets#Illumina|Illumina]]</li><br />
<li>[[Datasets#Sanger|Sanger]]</li><br />
<li>[[Datasets#Roche.2F454|Roche/454]]</li><br />
</ul><br />
</li><br />
<li>[[Datasets#Microarrays|Microarrays]]<br />
</ul><br />
<br />
== Lab life ==<br />
<ul><br />
<li>[[Lab_photos|Lab photos]]</li><br />
<li>Further pictures can be found in <b>/biodata/groups/crtd_tanaka/LabFun/</b></li><br />
<li>The recepies for Heino's farewell present can be found under <b>/biodata/groups/crtd_tanaka/LabFun/Heino's farewell present/</b></li><br />
<li>The video of the visit of the EU commissioner can be found under <b>/biodata/groups/crtd_tanaka/LabFun/</b></li><br />
</ul></div>
Serghein
https://wiki.tanakalab.org/index.php?title=Literature&diff=242
Literature
2013-02-07T20:32:34Z
<p>Serghein: /* Publications */</p>
<hr />
<div>== Theses ==<br />
{| class="wikitable sortable"<br />
!style="width: 650px" | Title<br />
!style="width: 250px" | Author<br />
!style="width: 50px" | Year<br />
!style="width: 200px" | Type<br />
|-<br />
|[[Media:Thesis Yu Zhu.pdf|Reconstitution of three-dimensional neuroepithelia from mouse and human pluripotent stem cells]]<br />
|Yu Zhu<br />
|2012<br />
|PhD thesis<br />
|-<br />
|[[Media:Master_Thesis_Plyasunova.pdf|Making transgenic axolotl for lineage tracing of connective tissue during limb regeneration]]<br />
|Liubov Plyasunova<br />
|2012<br />
|Master's thesis<br />
|}<br />
<br />
== Publications ==<br />
{| class="wikitable sortable"<br />
!style="width: 650px" | Title<br />
!style="width: 250px" | First author<br />
!style="width: 50px" | Year<br />
!style="width: 250px" | Journal<br />
|-<br />
|[[Media:YZ_2013.pdf|3D Neuroepithelial Culture from hESCs and Its Use for Quantitative Conversion to RPE]]<br />
|Yu Zhu<br />
|2013<br />
|PLOS ONE<br />
|-<br />
|[[Media:PM_2012.pdf|Regeneration: The ultimate example of wound healing]]<br />
|Prayag Murawala<br />
|2012<br />
|Seminars in Cell & Developmental Biology<br />
|}</div>
Serghein
https://wiki.tanakalab.org/index.php?title=File:YZ_2013.pdf&diff=241
File:YZ 2013.pdf
2013-02-07T20:32:06Z
<p>Serghein: </p>
<hr />
<div></div>
Serghein
https://wiki.tanakalab.org/index.php?title=Literature&diff=240
Literature
2013-02-07T20:27:43Z
<p>Serghein: /* Publications */</p>
<hr />
<div>== Theses ==<br />
{| class="wikitable sortable"<br />
!style="width: 650px" | Title<br />
!style="width: 250px" | Author<br />
!style="width: 50px" | Year<br />
!style="width: 200px" | Type<br />
|-<br />
|[[Media:Thesis Yu Zhu.pdf|Reconstitution of three-dimensional neuroepithelia from mouse and human pluripotent stem cells]]<br />
|Yu Zhu<br />
|2012<br />
|PhD thesis<br />
|-<br />
|[[Media:Master_Thesis_Plyasunova.pdf|Making transgenic axolotl for lineage tracing of connective tissue during limb regeneration]]<br />
|Liubov Plyasunova<br />
|2012<br />
|Master's thesis<br />
|}<br />
<br />
== Publications ==<br />
{| class="wikitable sortable"<br />
!style="width: 650px" | Title<br />
!style="width: 250px" | First author<br />
!style="width: 50px" | Year<br />
!style="width: 250px" | Journal<br />
|-<br />
|[[Media:3D_Neuroepithelial_Culture_from_hESCs_and_Its_Use_for_Quantitative_Conversion_to_RPE.pdf|3D Neuroepithelial Culture from hESCs and Its Use for Quantitative Conversion to RPE]]<br />
|Yu Zhu<br />
|2013<br />
|PLOS ONE<br />
|-<br />
|[[Media:PM_2012.pdf|Regeneration: The ultimate example of wound healing]]<br />
|Prayag Murawala<br />
|2012<br />
|Seminars in Cell & Developmental Biology<br />
|}</div>
Serghein
https://wiki.tanakalab.org/index.php?title=Datasets&diff=230
Datasets
2013-02-01T12:44:40Z
<p>Serghein: /* Illumina */</p>
<hr />
<div>== Sequences ==<br />
=== Illumina ===<br />
The data can be found under <b>//biodata/groups/crtd_tanaka/LabData/Sequencing/Illumina</b>.<br />
{| class="wikitable sortable"<br />
!style="width: 200px" class="unsortable" | Name<br />
!style="width: 300px" class="unsortable" | Description<br />
!style="width: 200px" | Tissue<br />
!style="width: 90px" class="unsortable" | Type<br />
!style="width: 80px" class="unsortable" | Read length<br />
!style="width: 100px" class="unsortable"| Fragment size<br />
!style="width: 150px" | Reads<br />
!style="width: 100px" class="unsortable" | Format<br />
!style="width: 200px" class="unsortable" | Location<br />
!style="width: 100px" | Author<br />
!style="width: 300px" class="unsortable" | Remarks<br />
|-<br />
|Mature spinal cord<br />
|Mature axolotl spinal cord<br />
|Spinal cord<br />
|Paired-ended<br />
|100bp<br />
|200-250bp<br />
|65,753,941<br />
|FastQ<br />
|SpinalCord/mSC.fastq.tar.gz<br />
|Akira Tazaki<br />
|<br />
|- <br />
|Injured spinal cord<br />
|Injured axolotl spinal cord, 6dpi<br />
|Spinal cord<br />
|Paired-ended<br />
|100bp<br />
|200-250bp<br />
|78,459,950<br />
|FastQ<br />
|SpinalCord/6diSC.fastq.tar.gz<br />
|Akira Tazaki<br />
|<br />
|-<br />
|Mature spinal cord<br />
|Mature axolotl spinal cord, replicate 2, crossing 142x5<br />
|Spinal cord<br />
|Paired-ended<br />
|100bp<br />
|180bp<br />
|101,769,559<br />
|FastQ<br />
|SpinalCord/mSC_142x5.fastq.tar.gz<br />
|Akira Tazaki<br />
|Due to a sequencer failure only the first 66 bases are safe<br />
|- <br />
|Mature spinal cord<br />
|Mature axolotl spinal cord, replicate 3, crossing 96x6<br />
|Spinal cord<br />
|Paired-ended<br />
|100bp<br />
|180bp<br />
|95,946,545<br />
|FastQ<br />
|SpinalCord/mSC_96x6.fastq.tar.gz<br />
|Akira Tazaki<br />
|Due to a sequencer failure only the first 66 bases are safe<br />
|- <br />
|Injured spinal cord<br />
|Injured axolotl spinal cord, 6dpi, replicate 2, crossing 142x5<br />
|Spinal cord<br />
|Paired-ended<br />
|100bp<br />
|180bp<br />
|96,626,387<br />
|FastQ<br />
|SpinalCord/6diSC_142x5.fastq.tar.gz<br />
|Akira Tazaki<br />
|Due to a sequencer failure only the first 66 bases are safe<br />
|- <br />
|Injured spinal cord<br />
|Injured axolotl spinal cord, 6dpi, replicate 3, crossing 96x5<br />
|Spinal cord<br />
|Paired-ended<br />
|100bp<br />
|180bp<br />
|99,855,603<br />
|FastQ<br />
|SpinalCord/6diSC_96x5.fastq.tar.gz<br />
|Akira Tazaki<br />
|Due to a sequencer failure only the first 66 bases are safe<br />
|-<br />
|Mature limb<br />
|Mature axolotl forelimb<br />
|Limb<br />
|Single-ended<br />
|76bp<br />
|n/a<br />
|65,934,228<br />
|FastQ<br />
|Limb/Mature.fastq.tar.gz<br />
|Dunja Knapp<br />
|<br />
|-<br />
|Amputated limb (36h)<br />
|Amputated axolotl forelimb (36hpa)<br />
|Limb<br />
|Single-ended<br />
|76bp<br />
|n/a<br />
|65,250,768<br />
|FastQ<br />
|Limb/36h_amp.fastq.tar.gz<br />
|Dunja Knapp<br />
|<br />
|-<br />
|Amputated limb (72h)<br />
|Amputated axolotl forelimb (72hpa)<br />
|Limb<br />
|Single-ended<br />
|76bp<br />
|n/a<br />
|62,970,898<br />
|FastQ<br />
|Limb/72h_amp.fastq.tar.gz<br />
|Dunja Knapp<br />
|<br />
|-<br />
|Lateral wound (36h)<br />
|Injured (lateral wound) axolotl forelimb (36hpw)<br />
|Limb<br />
|Single-ended<br />
|76bp<br />
|n/a<br />
|66,361,470<br />
|FastQ<br />
|Limb/36h_lw.fastq.tar.gz<br />
|Dunja Knapp<br />
|<br />
|-<br />
|Lateral wound (72h)<br />
|Injured (lateral wound) axolotl forelimb (72hpw)<br />
|Limb<br />
|Single-ended<br />
|76bp<br />
|n/a<br />
|64,133,834<br />
|FastQ<br />
|Limb/72h_lw.fastq.tar.gz<br />
|Dunja Knapp<br />
|<br />
|-<br />
|LPM-transplant<br />
|Blastema samples of a LPM-transplanted animal: mature and 1dpa<br />
|Limb blastema<br />
|Single-ended<br />
|<br />
|180bp<br />
|<ul><li>Mature: 35,982,029</li><li>1dpa: 39,824,276</li></ul><br />
|FastQ<br />
|LPM/An3.fastq.tar.gz<br />
|Prayag Murawala/Dunja Knapp<br />
|GFP-labeled LPM was transplanted to a white-host embryo. The limb of the host was amputated and the blastema sample was collected.<br />
|-<br />
|LPM-transplant<br />
|Blastema samples of a LPM-transplanted animal: mature and 10dpa<br />
|Limb blastema<br />
|Single-ended<br />
|<br />
|180bp<br />
|<ul><li>Mature: 47,155,937</li><li>10dpa: 40,468,959</li></ul><br />
|FastQ<br />
|LPM/An4.fastq.tar.gz<br />
|Prayag Murawala/Dunja Knapp<br />
|GFP-labeled LPM was transplanted to a white-host embryo. The limb of the host was amputated and the blastema sample was collected.<br />
|-<br />
|LPM-transplant<br />
|Blastema samples of a LPM-transplanted animal: mature and 5dpa<br />
|Limb blastema<br />
|Single-ended<br />
|<br />
|180bp<br />
|<ul><li>Mature: 38,879,295</li><li>5dpa: 33,775,319</li></ul><br />
|FastQ<br />
|LPM/An6.fastq.tar.gz<br />
|Prayag Murawala/Dunja Knapp<br />
|GFP-labeled LPM was transplanted to a white-host embryo. The limb of the host was amputated and the blastema sample was collected.<br />
|-<br />
|LPM-transplant<br />
|Blastema samples of a LPM-transplanted animal: mature and 7dpa<br />
|Limb blastema<br />
|Single-ended<br />
|<br />
|180bp<br />
|<ul><li>Mature: 52,385,146</li><li>7dpa: 54,639,187</li></ul><br />
|FastQ<br />
|LPM/An7.fastq.tar.gz<br />
|Prayag Murawala/Dunja Knapp<br />
|GFP-labeled LPM was transplanted to a white-host embryo. The limb of the host was amputated and the blastema sample was collected. <br />
|-<br />
|LPM-transplant<br />
|Blastema samples of a LPM-transplanted animal: mature and 3dpa<br />
|Limb blastema<br />
|Single-ended<br />
|<br />
|180bp<br />
|<ul><li>Mature: 69,327,682</li><li>3dpa: 52,633,592</li></ul><br />
|FastQ<br />
|LPM/An8.fastq.tar.gz<br />
|Prayag Murawala/Dunja Knapp<br />
|GFP-labeled LPM was transplanted to a white-host embryo. The limb of the host was amputated and the blastema sample was collected.<br />
|}<br />
<br />
Unsorted Illumina data can be found under <b>//biodata/groups/crtd_tanaka/LabData/Sequencing/Illumina/unsorted</b>.<br /><br />
For some of the data sets quality check was performed using FastQC. The statistics can be found under <b>//biodata/groups/crtd_tanaka/LabData/Sequencing/Illumina/qualitycheck</b>.<br />
<br />
=== Sanger ===<br />
The data can be found under <b>//biodata/groups/crtd_tanaka/LabData/Sequencing/Sanger</b>.<br />
{| class="wikitable sortable"<br />
!style="width: 200px" class="unsortable" | Name<br />
!style="width: 300px" class="unsortable" | Description<br />
!style="width: 200px" | Tissue<br />
!style="width: 200px" | Sequences<br />
!style="width: 300px" class="unsortable" | Location<br />
!style="width: 100px" | Author<br />
!style="width: 300px" class="unsortable" | Remarks<br />
|-<br />
|LimbBlastema<br />
|Limb blastema library<br />
|Limb blastema<br />
|20160 (RSD) / 15648 (SCF)<br />
|<ul><li>SCF files: LimbBlastema/LB_SCF.gz</li><li>RSD files: LimbBlastema/LB_RSD.gz</li></ul><br />
|Akira Tazaki<br />
|<br />
|-<br />
|NeuraTube<br />
|Neural tube library<br />
|Teural tube<br />
|4896 (RSD) / 7905 (SCF)<br />
|<ul><li>SCF files: NeuralTube/NT_SCF.gz</li><li>RSD files: NeuralTube/NT_RSD.gz</li></ul><br />
|Akira Tazaki<br />
|<br />
|}<br />
<br />
=== Roche/454 ===<br />
The data can be found under <b>//biodata/groups/crtd_tanaka/LabData/Sequencing/454</b>.<br />
{| class="wikitable"<br />
!style="width: 200px" | Name<br />
!style="width: 300px" | Description<br />
!style="width: 200px" | Tissue<br />
!style="width: 200px" | Reads<br />
!style="width: 200px" | Format<br />
!style="width: 300px" | Location<br />
!style="width: 100px" | Author<br />
!style="width: 300px" | Remarks<br />
|-<br />
|454<br />
|Mixed 454<br />
|Mixed<br />
|1,208,954<br />
|Fasta/Qual<br />
|Ax_454.tar.gz<br />
|n/a<br />
|}<br />
<br />
== Microarrays ==<br />
The data can be found under <b>//biodata/groups/crtd_tanaka/LabData/Microarrays</b>. Also consult the file <b>Contents.txt</b> in the experiment directory for more details. The raw data (*.tiff) files can be found in the subdirectory <b>Raw</b> in the experiment directory.<br />
{| class="wikitable"<br />
!style="width: 200px" | Name<br />
!style="width: 300px" | Description<br />
!style="width: 300px" | Timepoints<br />
!style="width: 200px" | Tissue<br />
!style="width: 110px" | Array type<br />
!style="width: 250px" | Location<br />
!style="width: 100px" | Author<br />
!style="width: 300px" | Remarks<br />
|-<br />
|Fin vs bulk<br />
|Timecourse microarray experiment using fin and bulk tissue<br />
|0, 1d, 3d<br />
|Mature tail: fin and bulk<br />
|Agilent, 44000<br />
|Fin_vs_bulk<br />
|Eugeniu Nacu<br />
|<br />
|-<br />
|Tail timecourse<br />
|Timecourse microarray experiment using tail<br />
|0, 3h, 6h, 12h, 18h, 24h, 36h, 48h, 72h, 120h, 168h, 288h<br />
|Mature tail<br />
|Agilent, 44000<br />
|Tail_timecourse<br />
|Eugeniu Nacu<br />
|<br />
|-<br />
|Limb timecourse<br />
|Timecourse microarray experiment using limb<br />
|0, 3h, 6h, 9h, 12h, 24h, 36h, 52h, 72h, 120h, 168h, 288h, 528h<br />
|Mature limb and limb bud<br />
|Agilent, 44000<br />
|Limb_timecourse<br />
|Dunja Knapp<br />
|<br />
|}</div>
Serghein
https://wiki.tanakalab.org/index.php?title=Datasets&diff=229
Datasets
2013-02-01T12:44:05Z
<p>Serghein: /* Illumina */</p>
<hr />
<div>== Sequences ==<br />
=== Illumina ===<br />
The data can be found under <b>//biodata/groups/crtd_tanaka/LabData/Sequencing/Illumina</b>.<br />
{| class="wikitable sortable"<br />
!style="width: 200px" class="unsortable" | Name<br />
!style="width: 300px" class="unsortable" | Description<br />
!style="width: 200px" | Tissue<br />
!style="width: 90px" class="unsortable" | Type<br />
!style="width: 80px" class="unsortable" | Read length<br />
!style="width: 100px" class="unsortable"| Fragment size<br />
!style="width: 150px" | Reads<br />
!style="width: 100px" class="unsortable" | Format<br />
!style="width: 200px" class="unsortable" | Location<br />
!style="width: 100px" | Author<br />
!style="width: 300px" class="unsortable" | Remarks<br />
|-<br />
|Mature spinal cord<br />
|Mature axolotl spinal cord<br />
|Spinal cord<br />
|Paired-ended<br />
|100bp<br />
|200-250bp<br />
|65,753,941<br />
|FastQ<br />
|SpinalCord/mSC.fastq.tar.gz<br />
|Akira Tazaki<br />
|<br />
|- <br />
|Injured spinal cord<br />
|Injured axolotl spinal cord, 6dpi<br />
|Spinal cord<br />
|Paired-ended<br />
|100bp<br />
|200-250bp<br />
|78,459,950<br />
|FastQ<br />
|SpinalCord/6diSC.fastq.tar.gz<br />
|Akira Tazaki<br />
|<br />
|-<br />
|Mature spinal cord<br />
|Mature axolotl spinal cord, replicate 2, crossing 142x5<br />
|Spinal cord<br />
|Paired-ended<br />
|100bp<br />
|180bp<br />
|101,769,559<br />
|FastQ<br />
|SpinalCord/mSC_142x5.fastq.tar.gz<br />
|Akira Tazaki<br />
|Due to a sequencer failure only the first 66 bases are safe<br />
|- <br />
|Mature spinal cord<br />
|Mature axolotl spinal cord, replicate 3, crossing 96x6<br />
|Spinal cord<br />
|Paired-ended<br />
|100bp<br />
|180bp<br />
|95,946,545<br />
|FastQ<br />
|SpinalCord/mSC_96x6.fastq.tar.gz<br />
|Akira Tazaki<br />
|Due to a sequencer failure only the first 66 bases are safe<br />
|- <br />
|Injured spinal cord<br />
|Injured axolotl spinal cord, 6dpi, replicate 2, crossing 142x5<br />
|Spinal cord<br />
|Paired-ended<br />
|100bp<br />
|180bp<br />
|96,626,387<br />
|FastQ<br />
|SpinalCord/6diSC_142x5.fastq.tar.gz<br />
|Akira Tazaki<br />
|Due to a sequencer failure only the first 66 bases are safe<br />
|- <br />
|Injured spinal cord<br />
|Injured axolotl spinal cord, 6dpi, replicate 3, crossing 96x5<br />
|Spinal cord<br />
|Paired-ended<br />
|100bp<br />
|180bp<br />
|99,855,603<br />
|FastQ<br />
|SpinalCord/6diSC_96x5.fastq.tar.gz<br />
|Akira Tazaki<br />
|Due to a sequencer failure only the first 66 bases are safe<br />
|-<br />
|Mature limb<br />
|Mature axolotl forelimb<br />
|Limb<br />
|Single-ended<br />
|76bp<br />
|n/a<br />
|65,934,228<br />
|FastQ<br />
|Limb/Mature.fastq.tar.gz<br />
|Dunja Knapp<br />
|<br />
|-<br />
|Amputated limb (36h)<br />
|Amputated axolotl forelimb (36hpa)<br />
|Limb<br />
|Single-ended<br />
|76bp<br />
|n/a<br />
|65,250,768<br />
|FastQ<br />
|Limb/36h_amp.fastq.tar.gz<br />
|Dunja Knapp<br />
|<br />
|-<br />
|Amputated limb (72h)<br />
|Amputated axolotl forelimb (72hpa)<br />
|Limb<br />
|Single-ended<br />
|76bp<br />
|n/a<br />
|62,970,898<br />
|FastQ<br />
|Limb/72h_amp.fastq.tar.gz<br />
|Dunja Knapp<br />
|<br />
|-<br />
|Lateral wound (36h)<br />
|Injured (lateral wound) axolotl forelimb (36hpw)<br />
|Limb<br />
|Single-ended<br />
|76bp<br />
|n/a<br />
|66,361,470<br />
|FastQ<br />
|Limb/36h_lw.fastq.tar.gz<br />
|Dunja Knapp<br />
|<br />
|-<br />
|Lateral wound (72h)<br />
|Injured (lateral wound) axolotl forelimb (72hpw)<br />
|Limb<br />
|Single-ended<br />
|76bp<br />
|n/a<br />
|64,133,834<br />
|FastQ<br />
|Limb/72h_lw.fastq.tar.gz<br />
|Dunja Knapp<br />
|<br />
|-<br />
|LPM-transplant<br />
|Blastema samples of a LPM-transplanted animal: mature and 1dpa<br />
|Limb blastema<br />
|Single-ended<br />
|<br />
|180bp<br />
|<ul><li>Mature: 35,982,029</li><li>1dpa: 39,824,276</li></ul><br />
|FastQ<br />
|LPM/An3.fastq.tar.gz<br />
|Prayag Murawala/Dunja Knapp<br />
|GFP-labeled LPM was transplanted to a white-host embryo. The limb of the host was amputated and the blastema sample was collected.<br />
|-<br />
|LPM-transplant<br />
|Blastema samples of a LPM-transplanted animal: mature and 10dpa<br />
|Limb blastema<br />
|Single-ended<br />
|<br />
|180bp<br />
|<ul><li>Mature: 47,155,937</li><li>10dpa: 40,468,959</li></ul><br />
|FastQ<br />
|LPM/An4.fastq.tar.gz<br />
|Prayag Murawala/Dunja Knapp<br />
|GFP-labeled LPM was transplanted to a white-host embryo. The limb of the host was amputated and the blastema sample was collected.<br />
|-<br />
|LPM-transplant<br />
|Blastema samples of a LPM-transplanted animal: mature and 5dpa<br />
|Limb blastema<br />
|Single-ended<br />
|<br />
|180bp<br />
|<ul><li>Mature: 38,879,295</li><li>5dpa: 33,775,319</li></ul><br />
|FastQ<br />
|LPM/An6.fastq.tar.gz<br />
|Prayag Murawala/Dunja Knapp<br />
|GFP-labeled LPM was transplanted to a white-host embryo. The limb of the host was amputated and the blastema sample was collected.<br />
|-<br />
|LPM-transplant<br />
|Blastema samples of a LPM-transplanted animal: mature and 7dpa<br />
|Limb blastema<br />
|Single-ended<br />
|<br />
|180bp<br />
|<ul><li>Mature: 52,385,146</li><li>7dpa: 54,639,187</li></ul><br />
|FastQ<br />
|LPM/An7.fastq.tar.gz<br />
|Prayag Murawala/Dunja Knapp<br />
|GFP-labeled LPM was transplanted to a white-host embryo. The limb of the host was amputated and the blastema sample was collected. <br />
|-<br />
|LPM-transplant<br />
|Blastema samples of a LPM-transplanted animal: mature and 3dpa<br />
|Limb blastema<br />
|Single-ended<br />
|<br />
|180bp<br />
|<ul><li>Mature: 69,327,682</li><li>3dpa: 52,633,592</li></ul><br />
|FastQ<br />
|LPM/An8.fastq.tar.gz<br />
|Prayag Murawala/Dunja Knapp<br />
|GFP-labeled LPM was transplanted to a white-host embryo. The limb of the host was amputated and the blastema sample was collected.<br />
|}<br />
<br />
Unsorted Illumina data can be found under <b>//biodata/groups/crtd_tanaka/LabData/Sequencing/Illumina/unsorted</b>.<br />
For some of the data sets quality check was performed using FastQC. The statistics can be found under <b>//biodata/groups/crtd_tanaka/LabData/Sequencing/Illumina/qualitycheck</b>.<br />
<br />
=== Sanger ===<br />
The data can be found under <b>//biodata/groups/crtd_tanaka/LabData/Sequencing/Sanger</b>.<br />
{| class="wikitable sortable"<br />
!style="width: 200px" class="unsortable" | Name<br />
!style="width: 300px" class="unsortable" | Description<br />
!style="width: 200px" | Tissue<br />
!style="width: 200px" | Sequences<br />
!style="width: 300px" class="unsortable" | Location<br />
!style="width: 100px" | Author<br />
!style="width: 300px" class="unsortable" | Remarks<br />
|-<br />
|LimbBlastema<br />
|Limb blastema library<br />
|Limb blastema<br />
|20160 (RSD) / 15648 (SCF)<br />
|<ul><li>SCF files: LimbBlastema/LB_SCF.gz</li><li>RSD files: LimbBlastema/LB_RSD.gz</li></ul><br />
|Akira Tazaki<br />
|<br />
|-<br />
|NeuraTube<br />
|Neural tube library<br />
|Teural tube<br />
|4896 (RSD) / 7905 (SCF)<br />
|<ul><li>SCF files: NeuralTube/NT_SCF.gz</li><li>RSD files: NeuralTube/NT_RSD.gz</li></ul><br />
|Akira Tazaki<br />
|<br />
|}<br />
<br />
=== Roche/454 ===<br />
The data can be found under <b>//biodata/groups/crtd_tanaka/LabData/Sequencing/454</b>.<br />
{| class="wikitable"<br />
!style="width: 200px" | Name<br />
!style="width: 300px" | Description<br />
!style="width: 200px" | Tissue<br />
!style="width: 200px" | Reads<br />
!style="width: 200px" | Format<br />
!style="width: 300px" | Location<br />
!style="width: 100px" | Author<br />
!style="width: 300px" | Remarks<br />
|-<br />
|454<br />
|Mixed 454<br />
|Mixed<br />
|1,208,954<br />
|Fasta/Qual<br />
|Ax_454.tar.gz<br />
|n/a<br />
|}<br />
<br />
== Microarrays ==<br />
The data can be found under <b>//biodata/groups/crtd_tanaka/LabData/Microarrays</b>. Also consult the file <b>Contents.txt</b> in the experiment directory for more details. The raw data (*.tiff) files can be found in the subdirectory <b>Raw</b> in the experiment directory.<br />
{| class="wikitable"<br />
!style="width: 200px" | Name<br />
!style="width: 300px" | Description<br />
!style="width: 300px" | Timepoints<br />
!style="width: 200px" | Tissue<br />
!style="width: 110px" | Array type<br />
!style="width: 250px" | Location<br />
!style="width: 100px" | Author<br />
!style="width: 300px" | Remarks<br />
|-<br />
|Fin vs bulk<br />
|Timecourse microarray experiment using fin and bulk tissue<br />
|0, 1d, 3d<br />
|Mature tail: fin and bulk<br />
|Agilent, 44000<br />
|Fin_vs_bulk<br />
|Eugeniu Nacu<br />
|<br />
|-<br />
|Tail timecourse<br />
|Timecourse microarray experiment using tail<br />
|0, 3h, 6h, 12h, 18h, 24h, 36h, 48h, 72h, 120h, 168h, 288h<br />
|Mature tail<br />
|Agilent, 44000<br />
|Tail_timecourse<br />
|Eugeniu Nacu<br />
|<br />
|-<br />
|Limb timecourse<br />
|Timecourse microarray experiment using limb<br />
|0, 3h, 6h, 9h, 12h, 24h, 36h, 52h, 72h, 120h, 168h, 288h, 528h<br />
|Mature limb and limb bud<br />
|Agilent, 44000<br />
|Limb_timecourse<br />
|Dunja Knapp<br />
|<br />
|}</div>
Serghein
https://wiki.tanakalab.org/index.php?title=Datasets&diff=228
Datasets
2013-01-31T23:15:12Z
<p>Serghein: /* Illumina */</p>
<hr />
<div>== Sequences ==<br />
=== Illumina ===<br />
The data can be found under <b>//biodata/groups/crtd_tanaka/LabData/Sequencing/Illumina</b>.<br />
{| class="wikitable sortable"<br />
!style="width: 200px" class="unsortable" | Name<br />
!style="width: 300px" class="unsortable" | Description<br />
!style="width: 200px" | Tissue<br />
!style="width: 90px" class="unsortable" | Type<br />
!style="width: 80px" class="unsortable" | Read length<br />
!style="width: 100px" class="unsortable"| Fragment size<br />
!style="width: 150px" | Reads<br />
!style="width: 100px" class="unsortable" | Format<br />
!style="width: 200px" class="unsortable" | Location<br />
!style="width: 100px" | Author<br />
!style="width: 300px" class="unsortable" | Remarks<br />
|-<br />
|Mature spinal cord<br />
|Mature axolotl spinal cord<br />
|Spinal cord<br />
|Paired-ended<br />
|100bp<br />
|200-250bp<br />
|65,753,941<br />
|FastQ<br />
|SpinalCord/mSC.fastq.tar.gz<br />
|Akira Tazaki<br />
|<br />
|- <br />
|Injured spinal cord<br />
|Injured axolotl spinal cord, 6dpi<br />
|Spinal cord<br />
|Paired-ended<br />
|100bp<br />
|200-250bp<br />
|78,459,950<br />
|FastQ<br />
|SpinalCord/6diSC.fastq.tar.gz<br />
|Akira Tazaki<br />
|<br />
|-<br />
|Mature spinal cord<br />
|Mature axolotl spinal cord, replicate 2, crossing 142x5<br />
|Spinal cord<br />
|Paired-ended<br />
|100bp<br />
|180bp<br />
|101,769,559<br />
|FastQ<br />
|SpinalCord/mSC_142x5.fastq.tar.gz<br />
|Akira Tazaki<br />
|Due to a sequencer failure only the first 66 bases are safe<br />
|- <br />
|Mature spinal cord<br />
|Mature axolotl spinal cord, replicate 3, crossing 96x6<br />
|Spinal cord<br />
|Paired-ended<br />
|100bp<br />
|180bp<br />
|95,946,545<br />
|FastQ<br />
|SpinalCord/mSC_96x6.fastq.tar.gz<br />
|Akira Tazaki<br />
|Due to a sequencer failure only the first 66 bases are safe<br />
|- <br />
|Injured spinal cord<br />
|Injured axolotl spinal cord, 6dpi, replicate 2, crossing 142x5<br />
|Spinal cord<br />
|Paired-ended<br />
|100bp<br />
|180bp<br />
|96,626,387<br />
|FastQ<br />
|SpinalCord/6diSC_142x5.fastq.tar.gz<br />
|Akira Tazaki<br />
|Due to a sequencer failure only the first 66 bases are safe<br />
|- <br />
|Injured spinal cord<br />
|Injured axolotl spinal cord, 6dpi, replicate 3, crossing 96x5<br />
|Spinal cord<br />
|Paired-ended<br />
|100bp<br />
|180bp<br />
|99,855,603<br />
|FastQ<br />
|SpinalCord/6diSC_96x5.fastq.tar.gz<br />
|Akira Tazaki<br />
|Due to a sequencer failure only the first 66 bases are safe<br />
|-<br />
|Mature limb<br />
|Mature axolotl forelimb<br />
|Limb<br />
|Single-ended<br />
|76bp<br />
|n/a<br />
|65,934,228<br />
|FastQ<br />
|Limb/Mature.fastq.tar.gz<br />
|Dunja Knapp<br />
|<br />
|-<br />
|Amputated limb (36h)<br />
|Amputated axolotl forelimb (36hpa)<br />
|Limb<br />
|Single-ended<br />
|76bp<br />
|n/a<br />
|65,250,768<br />
|FastQ<br />
|Limb/36h_amp.fastq.tar.gz<br />
|Dunja Knapp<br />
|<br />
|-<br />
|Amputated limb (72h)<br />
|Amputated axolotl forelimb (72hpa)<br />
|Limb<br />
|Single-ended<br />
|76bp<br />
|n/a<br />
|62,970,898<br />
|FastQ<br />
|Limb/72h_amp.fastq.tar.gz<br />
|Dunja Knapp<br />
|<br />
|-<br />
|Lateral wound (36h)<br />
|Injured (lateral wound) axolotl forelimb (36hpw)<br />
|Limb<br />
|Single-ended<br />
|76bp<br />
|n/a<br />
|66,361,470<br />
|FastQ<br />
|Limb/36h_lw.fastq.tar.gz<br />
|Dunja Knapp<br />
|<br />
|-<br />
|Lateral wound (72h)<br />
|Injured (lateral wound) axolotl forelimb (72hpw)<br />
|Limb<br />
|Single-ended<br />
|76bp<br />
|n/a<br />
|64,133,834<br />
|FastQ<br />
|Limb/72h_lw.fastq.tar.gz<br />
|Dunja Knapp<br />
|<br />
|-<br />
|LPM-transplant<br />
|Blastema samples of a LPM-transplanted animal: mature and 1dpa<br />
|Limb blastema<br />
|Single-ended<br />
|<br />
|180bp<br />
|<ul><li>Mature: 35,982,029</li><li>1dpa: 39,824,276</li></ul><br />
|FastQ<br />
|LPM/An3.fastq.tar.gz<br />
|Prayag Murawala/Dunja Knapp<br />
|GFP-labeled LPM was transplanted to a white-host embryo. The limb of the host was amputated and the blastema sample was collected.<br />
|-<br />
|LPM-transplant<br />
|Blastema samples of a LPM-transplanted animal: mature and 10dpa<br />
|Limb blastema<br />
|Single-ended<br />
|<br />
|180bp<br />
|<ul><li>Mature: 47,155,937</li><li>10dpa: 40,468,959</li></ul><br />
|FastQ<br />
|LPM/An4.fastq.tar.gz<br />
|Prayag Murawala/Dunja Knapp<br />
|GFP-labeled LPM was transplanted to a white-host embryo. The limb of the host was amputated and the blastema sample was collected.<br />
|-<br />
|LPM-transplant<br />
|Blastema samples of a LPM-transplanted animal: mature and 5dpa<br />
|Limb blastema<br />
|Single-ended<br />
|<br />
|180bp<br />
|<ul><li>Mature: 38,879,295</li><li>5dpa: 33,775,319</li></ul><br />
|FastQ<br />
|LPM/An6.fastq.tar.gz<br />
|Prayag Murawala/Dunja Knapp<br />
|GFP-labeled LPM was transplanted to a white-host embryo. The limb of the host was amputated and the blastema sample was collected.<br />
|-<br />
|LPM-transplant<br />
|Blastema samples of a LPM-transplanted animal: mature and 7dpa<br />
|Limb blastema<br />
|Single-ended<br />
|<br />
|180bp<br />
|<ul><li>Mature: 52,385,146</li><li>7dpa: 54,639,187</li></ul><br />
|FastQ<br />
|LPM/An7.fastq.tar.gz<br />
|Prayag Murawala/Dunja Knapp<br />
|GFP-labeled LPM was transplanted to a white-host embryo. The limb of the host was amputated and the blastema sample was collected. <br />
|-<br />
|LPM-transplant<br />
|Blastema samples of a LPM-transplanted animal: mature and 3dpa<br />
|Limb blastema<br />
|Single-ended<br />
|<br />
|180bp<br />
|<ul><li>Mature: 69,327,682</li><li>3dpa: 52,633,592</li></ul><br />
|FastQ<br />
|LPM/An8.fastq.tar.gz<br />
|Prayag Murawala/Dunja Knapp<br />
|GFP-labeled LPM was transplanted to a white-host embryo. The limb of the host was amputated and the blastema sample was collected.<br />
|}<br />
<br />
Unsorted Illumina data can be found under <b>//biodata/groups/crtd_tanaka/LabData/Sequencing/Illumina/unsorted</b>.<br />
<br />
=== Sanger ===<br />
The data can be found under <b>//biodata/groups/crtd_tanaka/LabData/Sequencing/Sanger</b>.<br />
{| class="wikitable sortable"<br />
!style="width: 200px" class="unsortable" | Name<br />
!style="width: 300px" class="unsortable" | Description<br />
!style="width: 200px" | Tissue<br />
!style="width: 200px" | Sequences<br />
!style="width: 300px" class="unsortable" | Location<br />
!style="width: 100px" | Author<br />
!style="width: 300px" class="unsortable" | Remarks<br />
|-<br />
|LimbBlastema<br />
|Limb blastema library<br />
|Limb blastema<br />
|20160 (RSD) / 15648 (SCF)<br />
|<ul><li>SCF files: LimbBlastema/LB_SCF.gz</li><li>RSD files: LimbBlastema/LB_RSD.gz</li></ul><br />
|Akira Tazaki<br />
|<br />
|-<br />
|NeuraTube<br />
|Neural tube library<br />
|Teural tube<br />
|4896 (RSD) / 7905 (SCF)<br />
|<ul><li>SCF files: NeuralTube/NT_SCF.gz</li><li>RSD files: NeuralTube/NT_RSD.gz</li></ul><br />
|Akira Tazaki<br />
|<br />
|}<br />
<br />
=== Roche/454 ===<br />
The data can be found under <b>//biodata/groups/crtd_tanaka/LabData/Sequencing/454</b>.<br />
{| class="wikitable"<br />
!style="width: 200px" | Name<br />
!style="width: 300px" | Description<br />
!style="width: 200px" | Tissue<br />
!style="width: 200px" | Reads<br />
!style="width: 200px" | Format<br />
!style="width: 300px" | Location<br />
!style="width: 100px" | Author<br />
!style="width: 300px" | Remarks<br />
|-<br />
|454<br />
|Mixed 454<br />
|Mixed<br />
|1,208,954<br />
|Fasta/Qual<br />
|Ax_454.tar.gz<br />
|n/a<br />
|}<br />
<br />
== Microarrays ==<br />
The data can be found under <b>//biodata/groups/crtd_tanaka/LabData/Microarrays</b>. Also consult the file <b>Contents.txt</b> in the experiment directory for more details. The raw data (*.tiff) files can be found in the subdirectory <b>Raw</b> in the experiment directory.<br />
{| class="wikitable"<br />
!style="width: 200px" | Name<br />
!style="width: 300px" | Description<br />
!style="width: 300px" | Timepoints<br />
!style="width: 200px" | Tissue<br />
!style="width: 110px" | Array type<br />
!style="width: 250px" | Location<br />
!style="width: 100px" | Author<br />
!style="width: 300px" | Remarks<br />
|-<br />
|Fin vs bulk<br />
|Timecourse microarray experiment using fin and bulk tissue<br />
|0, 1d, 3d<br />
|Mature tail: fin and bulk<br />
|Agilent, 44000<br />
|Fin_vs_bulk<br />
|Eugeniu Nacu<br />
|<br />
|-<br />
|Tail timecourse<br />
|Timecourse microarray experiment using tail<br />
|0, 3h, 6h, 12h, 18h, 24h, 36h, 48h, 72h, 120h, 168h, 288h<br />
|Mature tail<br />
|Agilent, 44000<br />
|Tail_timecourse<br />
|Eugeniu Nacu<br />
|<br />
|-<br />
|Limb timecourse<br />
|Timecourse microarray experiment using limb<br />
|0, 3h, 6h, 9h, 12h, 24h, 36h, 52h, 72h, 120h, 168h, 288h, 528h<br />
|Mature limb and limb bud<br />
|Agilent, 44000<br />
|Limb_timecourse<br />
|Dunja Knapp<br />
|<br />
|}</div>
Serghein
https://wiki.tanakalab.org/index.php?title=Datasets&diff=227
Datasets
2013-01-31T23:13:03Z
<p>Serghein: /* Illumina */</p>
<hr />
<div>== Sequences ==<br />
=== Illumina ===<br />
The data can be found under <b>//biodata/groups/crtd_tanaka/LabData/Sequencing/Illumina</b>.<br />
{| class="wikitable sortable"<br />
!style="width: 200px" class="unsortable" | Name<br />
!style="width: 300px" class="unsortable" | Description<br />
!style="width: 200px" | Tissue<br />
!style="width: 90px" class="unsortable" | Type<br />
!style="width: 80px" class="unsortable" | Read length<br />
!style="width: 100px" class="unsortable"| Fragment size<br />
!style="width: 150px" | Reads<br />
!style="width: 100px" class="unsortable" | Format<br />
!style="width: 200px" class="unsortable" | Location<br />
!style="width: 100px" | Author<br />
!style="width: 300px" class="unsortable" | Remarks<br />
|-<br />
|Mature spinal cord<br />
|Mature axolotl spinal cord<br />
|Spinal cord<br />
|Paired-ended<br />
|100bp<br />
|200-250bp<br />
|65,753,941<br />
|FastQ<br />
|SpinalCord/mSC.fastq.tar.gz<br />
|Akira Tazaki<br />
|<br />
|- <br />
|Injured spinal cord<br />
|Injured axolotl spinal cord, 6dpi<br />
|Spinal cord<br />
|Paired-ended<br />
|100bp<br />
|200-250bp<br />
|78,459,950<br />
|FastQ<br />
|SpinalCord/6diSC.fastq.tar.gz<br />
|Akira Tazaki<br />
|<br />
|-<br />
|Mature spinal cord<br />
|Mature axolotl spinal cord, replicate 2, crossing 142x5<br />
|Spinal cord<br />
|Paired-ended<br />
|100bp<br />
|180bp<br />
|101,769,559<br />
|FastQ<br />
|SpinalCord/mSC_142x5.fastq.tar.gz<br />
|Akira Tazaki<br />
|Due to a sequencer failure only the first 66 bases are safe<br />
|- <br />
|Mature spinal cord<br />
|Mature axolotl spinal cord, replicate 3, crossing 96x6<br />
|Spinal cord<br />
|Paired-ended<br />
|100bp<br />
|180bp<br />
|95,946,545<br />
|FastQ<br />
|SpinalCord/mSC_96x6.fastq.tar.gz<br />
|Akira Tazaki<br />
|Due to a sequencer failure only the first 66 bases are safe<br />
|- <br />
|Injured spinal cord<br />
|Injured axolotl spinal cord, 6dpi, replicate 2, crossing 142x5<br />
|Spinal cord<br />
|Paired-ended<br />
|100bp<br />
|180bp<br />
|96,626,387<br />
|FastQ<br />
|SpinalCord/6diSC_142x5.fastq.tar.gz<br />
|Akira Tazaki<br />
|Due to a sequencer failure only the first 66 bases are safe<br />
|- <br />
|Injured spinal cord<br />
|Injured axolotl spinal cord, 6dpi, replicate 3, crossing 96x5<br />
|Spinal cord<br />
|Paired-ended<br />
|100bp<br />
|180bp<br />
|99,855,603<br />
|FastQ<br />
|SpinalCord/6diSC_96x5.fastq.tar.gz<br />
|Akira Tazaki<br />
|Due to a sequencer failure only the first 66 bases are safe<br />
|-<br />
|Mature limb<br />
|Mature axolotl forelimb<br />
|Limb<br />
|Single-ended<br />
|76bp<br />
|n/a<br />
|65,934,228<br />
|FastQ<br />
|Limb/Mature.fastq.tar.gz<br />
|Dunja Knapp<br />
|<br />
|-<br />
|Amputated limb (36h)<br />
|Amputated axolotl forelimb (36hpa)<br />
|Limb<br />
|Single-ended<br />
|76bp<br />
|n/a<br />
|65,250,768<br />
|FastQ<br />
|Limb/36h_amp.fastq.tar.gz<br />
|Dunja Knapp<br />
|<br />
|-<br />
|Amputated limb (72h)<br />
|Amputated axolotl forelimb (72hpa)<br />
|Limb<br />
|Single-ended<br />
|76bp<br />
|n/a<br />
|62,970,898<br />
|FastQ<br />
|Limb/72h_amp.fastq.tar.gz<br />
|Dunja Knapp<br />
|<br />
|-<br />
|Lateral wound (36h)<br />
|Injured (lateral wound) axolotl forelimb (36hpw)<br />
|Limb<br />
|Single-ended<br />
|76bp<br />
|n/a<br />
|66,361,470<br />
|FastQ<br />
|Limb/36h_lw.fastq.tar.gz<br />
|Dunja Knapp<br />
|<br />
|-<br />
|Lateral wound (72h)<br />
|Injured (lateral wound) axolotl forelimb (72hpw)<br />
|Limb<br />
|Single-ended<br />
|76bp<br />
|n/a<br />
|64,133,834<br />
|FastQ<br />
|Limb/72h_lw.fastq.tar.gz<br />
|Dunja Knapp<br />
|<br />
|-<br />
|LPM-transplant<br />
|Blastema samples of a LPM-transplanted animal: mature and 1dpa<br />
|Limb blastema<br />
|Single-ended<br />
|<br />
|180bp<br />
|<ul><li>Mature: 35,982,029</li><li>1dpa: 39,824,276</li></ul><br />
|FastQ<br />
|LPM/An3.fastq.tar.gz<br />
|Prayag Murawala/Dunja Knapp<br />
|GFP-labeled LPM was transplanted to a white-host embryo. The limb of the host was amputated and the blastema sample was collected.<br />
|-<br />
|LPM-transplant<br />
|Blastema samples of a LPM-transplanted animal: mature and 10dpa<br />
|Limb blastema<br />
|Single-ended<br />
|<br />
|180bp<br />
|<ul><li>Mature: 47,155,937</li><li>10dpa: 40,468,959</li></ul><br />
|FastQ<br />
|LPM/An4.fastq.tar.gz<br />
|Prayag Murawala/Dunja Knapp<br />
|GFP-labeled LPM was transplanted to a white-host embryo. The limb of the host was amputated and the blastema sample was collected.<br />
|-<br />
|LPM-transplant<br />
|Blastema samples of a LPM-transplanted animal: mature and 5dpa<br />
|Limb blastema<br />
|Single-ended<br />
|<br />
|180bp<br />
|<ul><li>Mature: 38,879,295</li><li>5dpa: 33,775,319</li></ul><br />
|FastQ<br />
|LPM/An6.fastq.tar.gz<br />
|Prayag Murawala/Dunja Knapp<br />
|GFP-labeled LPM was transplanted to a white-host embryo. The limb of the host was amputated and the blastema sample was collected.<br />
|-<br />
|LPM-transplant<br />
|Blastema samples of a LPM-transplanted animal: mature and 7dpa<br />
|Limb blastema<br />
|Single-ended<br />
|<br />
|180bp<br />
|<ul><li>Mature: 52,385,146</li><li>7dpa: 54,639,187</li></ul><br />
|FastQ<br />
|LPM/An7.fastq.tar.gz<br />
|Prayag Murawala/Dunja Knapp<br />
|GFP-labeled LPM was transplanted to a white-host embryo. The limb of the host was amputated and the blastema sample was collected. <br />
|-<br />
|LPM-transplant<br />
|Blastema samples of a LPM-transplanted animal: mature and 3dpa<br />
|Limb blastema<br />
|Single-ended<br />
|<br />
|180bp<br />
|<ul><li>Mature: 69,327,682</li><li>3dpa: 52,633,592</li></ul><br />
|FastQ<br />
|LPM/An8.fastq.tar.gz<br />
|Prayag Murawala/Dunja Knapp<br />
|GFP-labeled LPM was transplanted to a white-host embryo. The limb of the host was amputated and the blastema sample was collected.<br />
|}<br />
<br />
Unsorted Illumina data can be found under <b>//biodata/groups/crtd_tanaka/LabData/Sequencing/Illumina</b>.<br />
<br />
=== Sanger ===<br />
The data can be found under <b>//biodata/groups/crtd_tanaka/LabData/Sequencing/Sanger</b>.<br />
{| class="wikitable sortable"<br />
!style="width: 200px" class="unsortable" | Name<br />
!style="width: 300px" class="unsortable" | Description<br />
!style="width: 200px" | Tissue<br />
!style="width: 200px" | Sequences<br />
!style="width: 300px" class="unsortable" | Location<br />
!style="width: 100px" | Author<br />
!style="width: 300px" class="unsortable" | Remarks<br />
|-<br />
|LimbBlastema<br />
|Limb blastema library<br />
|Limb blastema<br />
|20160 (RSD) / 15648 (SCF)<br />
|<ul><li>SCF files: LimbBlastema/LB_SCF.gz</li><li>RSD files: LimbBlastema/LB_RSD.gz</li></ul><br />
|Akira Tazaki<br />
|<br />
|-<br />
|NeuraTube<br />
|Neural tube library<br />
|Teural tube<br />
|4896 (RSD) / 7905 (SCF)<br />
|<ul><li>SCF files: NeuralTube/NT_SCF.gz</li><li>RSD files: NeuralTube/NT_RSD.gz</li></ul><br />
|Akira Tazaki<br />
|<br />
|}<br />
<br />
=== Roche/454 ===<br />
The data can be found under <b>//biodata/groups/crtd_tanaka/LabData/Sequencing/454</b>.<br />
{| class="wikitable"<br />
!style="width: 200px" | Name<br />
!style="width: 300px" | Description<br />
!style="width: 200px" | Tissue<br />
!style="width: 200px" | Reads<br />
!style="width: 200px" | Format<br />
!style="width: 300px" | Location<br />
!style="width: 100px" | Author<br />
!style="width: 300px" | Remarks<br />
|-<br />
|454<br />
|Mixed 454<br />
|Mixed<br />
|1,208,954<br />
|Fasta/Qual<br />
|Ax_454.tar.gz<br />
|n/a<br />
|}<br />
<br />
== Microarrays ==<br />
The data can be found under <b>//biodata/groups/crtd_tanaka/LabData/Microarrays</b>. Also consult the file <b>Contents.txt</b> in the experiment directory for more details. The raw data (*.tiff) files can be found in the subdirectory <b>Raw</b> in the experiment directory.<br />
{| class="wikitable"<br />
!style="width: 200px" | Name<br />
!style="width: 300px" | Description<br />
!style="width: 300px" | Timepoints<br />
!style="width: 200px" | Tissue<br />
!style="width: 110px" | Array type<br />
!style="width: 250px" | Location<br />
!style="width: 100px" | Author<br />
!style="width: 300px" | Remarks<br />
|-<br />
|Fin vs bulk<br />
|Timecourse microarray experiment using fin and bulk tissue<br />
|0, 1d, 3d<br />
|Mature tail: fin and bulk<br />
|Agilent, 44000<br />
|Fin_vs_bulk<br />
|Eugeniu Nacu<br />
|<br />
|-<br />
|Tail timecourse<br />
|Timecourse microarray experiment using tail<br />
|0, 3h, 6h, 12h, 18h, 24h, 36h, 48h, 72h, 120h, 168h, 288h<br />
|Mature tail<br />
|Agilent, 44000<br />
|Tail_timecourse<br />
|Eugeniu Nacu<br />
|<br />
|-<br />
|Limb timecourse<br />
|Timecourse microarray experiment using limb<br />
|0, 3h, 6h, 9h, 12h, 24h, 36h, 52h, 72h, 120h, 168h, 288h, 528h<br />
|Mature limb and limb bud<br />
|Agilent, 44000<br />
|Limb_timecourse<br />
|Dunja Knapp<br />
|<br />
|}</div>
Serghein
https://wiki.tanakalab.org/index.php?title=Datasets&diff=226
Datasets
2013-01-31T15:51:41Z
<p>Serghein: /* Illumina */</p>
<hr />
<div>== Sequences ==<br />
=== Illumina ===<br />
The data can be found under <b>//biodata/groups/crtd_tanaka/LabData/Sequencing/Illumina</b>.<br />
{| class="wikitable sortable"<br />
!style="width: 200px" class="unsortable" | Name<br />
!style="width: 300px" class="unsortable" | Description<br />
!style="width: 200px" | Tissue<br />
!style="width: 90px" class="unsortable" | Type<br />
!style="width: 80px" class="unsortable" | Read length<br />
!style="width: 100px" class="unsortable"| Fragment size<br />
!style="width: 150px" | Reads<br />
!style="width: 100px" class="unsortable" | Format<br />
!style="width: 200px" class="unsortable" | Location<br />
!style="width: 100px" | Author<br />
!style="width: 300px" class="unsortable" | Remarks<br />
|-<br />
|Mature spinal cord<br />
|Mature axolotl spinal cord<br />
|Spinal cord<br />
|Paired-ended<br />
|100bp<br />
|200-250bp<br />
|65,753,941<br />
|FastQ<br />
|SpinalCord/mSC.fastq.tar.gz<br />
|Akira Tazaki<br />
|<br />
|- <br />
|Injured spinal cord<br />
|Injured axolotl spinal cord, 6dpi<br />
|Spinal cord<br />
|Paired-ended<br />
|100bp<br />
|200-250bp<br />
|78,459,950<br />
|FastQ<br />
|SpinalCord/6diSC.fastq.tar.gz<br />
|Akira Tazaki<br />
|<br />
|-<br />
|Mature spinal cord<br />
|Mature axolotl spinal cord, replicate 2, crossing 142x5<br />
|Spinal cord<br />
|Paired-ended<br />
|100bp<br />
|180bp<br />
|101,769,559<br />
|FastQ<br />
|SpinalCord/mSC_142x5.fastq.tar.gz<br />
|Akira Tazaki<br />
|Due to a sequencer failure only the first 66 bases are safe<br />
|- <br />
|Mature spinal cord<br />
|Mature axolotl spinal cord, replicate 3, crossing 96x6<br />
|Spinal cord<br />
|Paired-ended<br />
|100bp<br />
|180bp<br />
|95,946,545<br />
|FastQ<br />
|SpinalCord/mSC_96x6.fastq.tar.gz<br />
|Akira Tazaki<br />
|Due to a sequencer failure only the first 66 bases are safe<br />
|- <br />
|Injured spinal cord<br />
|Injured axolotl spinal cord, 6dpi, replicate 2, crossing 142x5<br />
|Spinal cord<br />
|Paired-ended<br />
|100bp<br />
|180bp<br />
|96,626,387<br />
|FastQ<br />
|SpinalCord/6diSC_142x5.fastq.tar.gz<br />
|Akira Tazaki<br />
|Due to a sequencer failure only the first 66 bases are safe<br />
|- <br />
|Injured spinal cord<br />
|Injured axolotl spinal cord, 6dpi, replicate 3, crossing 96x5<br />
|Spinal cord<br />
|Paired-ended<br />
|100bp<br />
|180bp<br />
|99,855,603<br />
|FastQ<br />
|SpinalCord/6diSC_96x5.fastq.tar.gz<br />
|Akira Tazaki<br />
|Due to a sequencer failure only the first 66 bases are safe<br />
|-<br />
|Mature limb<br />
|Mature axolotl forelimb<br />
|Limb<br />
|Single-ended<br />
|76bp<br />
|n/a<br />
|65,934,228<br />
|FastQ<br />
|Limb/Mature.fastq.tar.gz<br />
|Dunja Knapp<br />
|<br />
|-<br />
|Amputated limb (36h)<br />
|Amputated axolotl forelimb (36hpa)<br />
|Limb<br />
|Single-ended<br />
|76bp<br />
|n/a<br />
|65,250,768<br />
|FastQ<br />
|Limb/36h_amp.fastq.tar.gz<br />
|Dunja Knapp<br />
|<br />
|-<br />
|Amputated limb (72h)<br />
|Amputated axolotl forelimb (72hpa)<br />
|Limb<br />
|Single-ended<br />
|76bp<br />
|n/a<br />
|62,970,898<br />
|FastQ<br />
|Limb/72h_amp.fastq.tar.gz<br />
|Dunja Knapp<br />
|<br />
|-<br />
|Lateral wound (36h)<br />
|Injured (lateral wound) axolotl forelimb (36hpw)<br />
|Limb<br />
|Single-ended<br />
|76bp<br />
|n/a<br />
|66,361,470<br />
|FastQ<br />
|Limb/36h_lw.fastq.tar.gz<br />
|Dunja Knapp<br />
|<br />
|-<br />
|Lateral wound (72h)<br />
|Injured (lateral wound) axolotl forelimb (72hpw)<br />
|Limb<br />
|Single-ended<br />
|76bp<br />
|n/a<br />
|64,133,834<br />
|FastQ<br />
|Limb/72h_lw.fastq.tar.gz<br />
|Dunja Knapp<br />
|<br />
|-<br />
|LPM-transplant<br />
|Blastema samples of a LPM-transplanted animal: mature and 1dpa<br />
|Blastema<br />
|Single-ended<br />
|<br />
|180bp<br />
|<br />
|FastQ<br />
|LPM/An3.fastq.tar.gz<br />
|Prayag Murawala/Dunja Knapp<br />
|GFP-labeled LPM was transplanted to a white-host embryo. The limb of the host was amputated and the blastema sample was collected.<br />
|-<br />
|LPM-transplant<br />
|Blastema samples of a LPM-transplanted animal: mature and 10dpa<br />
|Blastema<br />
|Single-ended<br />
|<br />
|180bp<br />
|<br />
|FastQ<br />
|LPM/An4.fastq.tar.gz<br />
|Prayag Murawala/Dunja Knapp<br />
|GFP-labeled LPM was transplanted to a white-host embryo. The limb of the host was amputated and the blastema sample was collected.<br />
|-<br />
|LPM-transplant<br />
|Blastema samples of a LPM-transplanted animal: mature and 5dpa<br />
|Blastema<br />
|Single-ended<br />
|<br />
|180bp<br />
|<ul><li>Mature: 38,879,295</li><li>5dpa: 33,775,319</li></ul><br />
|FastQ<br />
|LPM/An6.fastq.tar.gz<br />
|Prayag Murawala/Dunja Knapp<br />
|GFP-labeled LPM was transplanted to a white-host embryo. The limb of the host was amputated and the blastema sample was collected.<br />
|-<br />
|LPM-transplant<br />
|Blastema samples of a LPM-transplanted animal: mature and 7dpa<br />
|Blastema<br />
|Single-ended<br />
|<br />
|180bp<br />
|<br />
|FastQ<br />
|LPM/An7.fastq.tar.gz<br />
|Prayag Murawala/Dunja Knapp<br />
|GFP-labeled LPM was transplanted to a white-host embryo. The limb of the host was amputated and the blastema sample was collected. <br />
|-<br />
|LPM-transplant<br />
|Blastema samples of a LPM-transplanted animal: mature and 3dpa<br />
|Blastema<br />
|Single-ended<br />
|<br />
|180bp<br />
|<br />
|FastQ<br />
|LPM/An8.fastq.tar.gz<br />
|Prayag Murawala/Dunja Knapp<br />
|GFP-labeled LPM was transplanted to a white-host embryo. The limb of the host was amputated and the blastema sample was collected.<br />
|}<br />
<br />
Unsorted Illumina data can be found under <b>//biodata/groups/crtd_tanaka/LabData/Sequencing/Illumina</b>.<br />
<br />
=== Sanger ===<br />
The data can be found under <b>//biodata/groups/crtd_tanaka/LabData/Sequencing/Sanger</b>.<br />
{| class="wikitable sortable"<br />
!style="width: 200px" class="unsortable" | Name<br />
!style="width: 300px" class="unsortable" | Description<br />
!style="width: 200px" | Tissue<br />
!style="width: 200px" | Sequences<br />
!style="width: 300px" class="unsortable" | Location<br />
!style="width: 100px" | Author<br />
!style="width: 300px" class="unsortable" | Remarks<br />
|-<br />
|LimbBlastema<br />
|Limb blastema library<br />
|Limb blastema<br />
|20160 (RSD) / 15648 (SCF)<br />
|<ul><li>SCF files: LimbBlastema/LB_SCF.gz</li><li>RSD files: LimbBlastema/LB_RSD.gz</li></ul><br />
|Akira Tazaki<br />
|<br />
|-<br />
|NeuraTube<br />
|Neural tube library<br />
|Teural tube<br />
|4896 (RSD) / 7905 (SCF)<br />
|<ul><li>SCF files: NeuralTube/NT_SCF.gz</li><li>RSD files: NeuralTube/NT_RSD.gz</li></ul><br />
|Akira Tazaki<br />
|<br />
|}<br />
<br />
=== Roche/454 ===<br />
The data can be found under <b>//biodata/groups/crtd_tanaka/LabData/Sequencing/454</b>.<br />
{| class="wikitable"<br />
!style="width: 200px" | Name<br />
!style="width: 300px" | Description<br />
!style="width: 200px" | Tissue<br />
!style="width: 200px" | Reads<br />
!style="width: 200px" | Format<br />
!style="width: 300px" | Location<br />
!style="width: 100px" | Author<br />
!style="width: 300px" | Remarks<br />
|-<br />
|454<br />
|Mixed 454<br />
|Mixed<br />
|1,208,954<br />
|Fasta/Qual<br />
|Ax_454.tar.gz<br />
|n/a<br />
|}<br />
<br />
== Microarrays ==<br />
The data can be found under <b>//biodata/groups/crtd_tanaka/LabData/Microarrays</b>. Also consult the file <b>Contents.txt</b> in the experiment directory for more details. The raw data (*.tiff) files can be found in the subdirectory <b>Raw</b> in the experiment directory.<br />
{| class="wikitable"<br />
!style="width: 200px" | Name<br />
!style="width: 300px" | Description<br />
!style="width: 300px" | Timepoints<br />
!style="width: 200px" | Tissue<br />
!style="width: 110px" | Array type<br />
!style="width: 250px" | Location<br />
!style="width: 100px" | Author<br />
!style="width: 300px" | Remarks<br />
|-<br />
|Fin vs bulk<br />
|Timecourse microarray experiment using fin and bulk tissue<br />
|0, 1d, 3d<br />
|Mature tail: fin and bulk<br />
|Agilent, 44000<br />
|Fin_vs_bulk<br />
|Eugeniu Nacu<br />
|<br />
|-<br />
|Tail timecourse<br />
|Timecourse microarray experiment using tail<br />
|0, 3h, 6h, 12h, 18h, 24h, 36h, 48h, 72h, 120h, 168h, 288h<br />
|Mature tail<br />
|Agilent, 44000<br />
|Tail_timecourse<br />
|Eugeniu Nacu<br />
|<br />
|-<br />
|Limb timecourse<br />
|Timecourse microarray experiment using limb<br />
|0, 3h, 6h, 9h, 12h, 24h, 36h, 52h, 72h, 120h, 168h, 288h, 528h<br />
|Mature limb and limb bud<br />
|Agilent, 44000<br />
|Limb_timecourse<br />
|Dunja Knapp<br />
|<br />
|}</div>
Serghein
https://wiki.tanakalab.org/index.php?title=Datasets&diff=225
Datasets
2013-01-31T15:22:37Z
<p>Serghein: /* Illumina */</p>
<hr />
<div>== Sequences ==<br />
=== Illumina ===<br />
The data can be found under <b>//biodata/groups/crtd_tanaka/LabData/Sequencing/Illumina</b>.<br />
{| class="wikitable sortable"<br />
!style="width: 200px" class="unsortable" | Name<br />
!style="width: 300px" class="unsortable" | Description<br />
!style="width: 200px" | Tissue<br />
!style="width: 90px" class="unsortable" | Type<br />
!style="width: 80px" class="unsortable" | Read length<br />
!style="width: 100px" class="unsortable"| Fragment size<br />
!style="width: 100px" | Reads<br />
!style="width: 100px" class="unsortable" | Format<br />
!style="width: 200px" class="unsortable" | Location<br />
!style="width: 100px" | Author<br />
!style="width: 300px" class="unsortable" | Remarks<br />
|-<br />
|Mature spinal cord<br />
|Mature axolotl spinal cord<br />
|Spinal cord<br />
|Paired-ended<br />
|100bp<br />
|n/a<br />
|65,753,941<br />
|FastQ<br />
|SpinalCord/mSC.fastq.tar.gz<br />
|Akira Tazaki<br />
|<br />
|- <br />
|Injured spinal cord<br />
|Injured axolotl spinal cord, 6dpi<br />
|Spinal cord<br />
|Paired-ended<br />
|100bp<br />
|n/a<br />
|78,459,950<br />
|FastQ<br />
|SpinalCord/6diSC.fastq.tar.gz<br />
|Akira Tazaki<br />
|<br />
|-<br />
|Mature spinal cord<br />
|Mature axolotl spinal cord, replicate 2, crossing 142x5<br />
|Spinal cord<br />
|Paired-ended<br />
|100bp<br />
|180bp<br />
|101,769,559<br />
|FastQ<br />
|SpinalCord/mSC_142x5.fastq.tar.gz<br />
|Akira Tazaki<br />
|Due to a sequencer failure only the first 66 bases are safe<br />
|- <br />
|Mature spinal cord<br />
|Mature axolotl spinal cord, replicate 3, crossing 96x6<br />
|Spinal cord<br />
|Paired-ended<br />
|100bp<br />
|180bp<br />
|95,946,545<br />
|FastQ<br />
|SpinalCord/mSC_96x6.fastq.tar.gz<br />
|Akira Tazaki<br />
|Due to a sequencer failure only the first 66 bases are safe<br />
|- <br />
|Injured spinal cord<br />
|Injured axolotl spinal cord, 6dpi, replicate 2, crossing 142x5<br />
|Spinal cord<br />
|Paired-ended<br />
|100bp<br />
|180bp<br />
|96,626,387<br />
|FastQ<br />
|SpinalCord/6diSC_142x5.fastq.tar.gz<br />
|Akira Tazaki<br />
|Due to a sequencer failure only the first 66 bases are safe<br />
|- <br />
|Injured spinal cord<br />
|Injured axolotl spinal cord, 6dpi, replicate 3, crossing 96x5<br />
|Spinal cord<br />
|Paired-ended<br />
|100bp<br />
|180bp<br />
|99,855,603<br />
|FastQ<br />
|SpinalCord/6diSC_96x5.fastq.tar.gz<br />
|Akira Tazaki<br />
|Due to a sequencer failure only the first 66 bases are safe<br />
|-<br />
|Mature limb<br />
|Mature axolotl forelimb<br />
|Limb<br />
|Single-ended<br />
|76bp<br />
|n/a<br />
|65,934,228<br />
|FastQ<br />
|Limb/Mature.fastq.tar.gz<br />
|Dunja Knapp<br />
|<br />
|-<br />
|Amputated limb (36h)<br />
|Amputated axolotl forelimb (36hpa)<br />
|Limb<br />
|Single-ended<br />
|76bp<br />
|n/a<br />
|65,250,768<br />
|FastQ<br />
|Limb/36h_amp.fastq.tar.gz<br />
|Dunja Knapp<br />
|<br />
|-<br />
|Amputated limb (72h)<br />
|Amputated axolotl forelimb (72hpa)<br />
|Limb<br />
|Single-ended<br />
|76bp<br />
|n/a<br />
|62,970,898<br />
|FastQ<br />
|Limb/72h_amp.fastq.tar.gz<br />
|Dunja Knapp<br />
|<br />
|-<br />
|Lateral wound (36h)<br />
|Injured (lateral wound) axolotl forelimb (36hpw)<br />
|Limb<br />
|Single-ended<br />
|76bp<br />
|n/a<br />
|66,361,470<br />
|FastQ<br />
|Limb/36h_lw.fastq.tar.gz<br />
|Dunja Knapp<br />
|<br />
|-<br />
|Lateral wound (72h)<br />
|Injured (lateral wound) axolotl forelimb (72hpw)<br />
|Limb<br />
|Single-ended<br />
|76bp<br />
|n/a<br />
|64,133,834<br />
|FastQ<br />
|Limb/72h_lw.fastq.tar.gz<br />
|Dunja Knapp<br />
|<br />
|-<br />
|LPM-transplant<br />
|Blastema samples of a LPM-transplanted animal: mature and 1dpa<br />
|Blastema<br />
|Single-ended<br />
|<br />
|180bp<br />
|<br />
|FastQ<br />
|LPM/An3.fastq.tar.gz<br />
|Prayag Murawala/Dunja Knapp<br />
|GFP-labeled LPM was transplanted to a white-host embryo. The limb of the host was amputated and the blastema sample was collected.<br />
|-<br />
|LPM-transplant<br />
|Blastema samples of a LPM-transplanted animal: mature and 10dpa<br />
|Blastema<br />
|Single-ended<br />
|<br />
|180bp<br />
|<br />
|FastQ<br />
|LPM/An4.fastq.tar.gz<br />
|Prayag Murawala/Dunja Knapp<br />
|GFP-labeled LPM was transplanted to a white-host embryo. The limb of the host was amputated and the blastema sample was collected.<br />
|-<br />
|LPM-transplant<br />
|Blastema samples of a LPM-transplanted animal: mature and 5dpa<br />
|Blastema<br />
|Single-ended<br />
|<br />
|180bp<br />
|<br />
|FastQ<br />
|LPM/An6.fastq.tar.gz<br />
|Prayag Murawala/Dunja Knapp<br />
|GFP-labeled LPM was transplanted to a white-host embryo. The limb of the host was amputated and the blastema sample was collected.<br />
|-<br />
|LPM-transplant<br />
|Blastema samples of a LPM-transplanted animal: mature and 7dpa<br />
|Blastema<br />
|Single-ended<br />
|<br />
|180bp<br />
|<br />
|FastQ<br />
|LPM/An7.fastq.tar.gz<br />
|Prayag Murawala/Dunja Knapp<br />
|GFP-labeled LPM was transplanted to a white-host embryo. The limb of the host was amputated and the blastema sample was collected. <br />
|-<br />
|LPM-transplant<br />
|Blastema samples of a LPM-transplanted animal: mature and 3dpa<br />
|Blastema<br />
|Single-ended<br />
|<br />
|180bp<br />
|<br />
|FastQ<br />
|LPM/An8.fastq.tar.gz<br />
|Prayag Murawala/Dunja Knapp<br />
|GFP-labeled LPM was transplanted to a white-host embryo. The limb of the host was amputated and the blastema sample was collected.<br />
|}<br />
<br />
Unsorted Illumina data can be found under <b>//biodata/groups/crtd_tanaka/LabData/Sequencing/Illumina</b>.<br />
<br />
=== Sanger ===<br />
The data can be found under <b>//biodata/groups/crtd_tanaka/LabData/Sequencing/Sanger</b>.<br />
{| class="wikitable sortable"<br />
!style="width: 200px" class="unsortable" | Name<br />
!style="width: 300px" class="unsortable" | Description<br />
!style="width: 200px" | Tissue<br />
!style="width: 200px" | Sequences<br />
!style="width: 300px" class="unsortable" | Location<br />
!style="width: 100px" | Author<br />
!style="width: 300px" class="unsortable" | Remarks<br />
|-<br />
|LimbBlastema<br />
|Limb blastema library<br />
|Limb blastema<br />
|20160 (RSD) / 15648 (SCF)<br />
|<ul><li>SCF files: LimbBlastema/LB_SCF.gz</li><li>RSD files: LimbBlastema/LB_RSD.gz</li></ul><br />
|Akira Tazaki<br />
|<br />
|-<br />
|NeuraTube<br />
|Neural tube library<br />
|Teural tube<br />
|4896 (RSD) / 7905 (SCF)<br />
|<ul><li>SCF files: NeuralTube/NT_SCF.gz</li><li>RSD files: NeuralTube/NT_RSD.gz</li></ul><br />
|Akira Tazaki<br />
|<br />
|}<br />
<br />
=== Roche/454 ===<br />
The data can be found under <b>//biodata/groups/crtd_tanaka/LabData/Sequencing/454</b>.<br />
{| class="wikitable"<br />
!style="width: 200px" | Name<br />
!style="width: 300px" | Description<br />
!style="width: 200px" | Tissue<br />
!style="width: 200px" | Reads<br />
!style="width: 200px" | Format<br />
!style="width: 300px" | Location<br />
!style="width: 100px" | Author<br />
!style="width: 300px" | Remarks<br />
|-<br />
|454<br />
|Mixed 454<br />
|Mixed<br />
|1,208,954<br />
|Fasta/Qual<br />
|Ax_454.tar.gz<br />
|n/a<br />
|}<br />
<br />
== Microarrays ==<br />
The data can be found under <b>//biodata/groups/crtd_tanaka/LabData/Microarrays</b>. Also consult the file <b>Contents.txt</b> in the experiment directory for more details. The raw data (*.tiff) files can be found in the subdirectory <b>Raw</b> in the experiment directory.<br />
{| class="wikitable"<br />
!style="width: 200px" | Name<br />
!style="width: 300px" | Description<br />
!style="width: 300px" | Timepoints<br />
!style="width: 200px" | Tissue<br />
!style="width: 110px" | Array type<br />
!style="width: 250px" | Location<br />
!style="width: 100px" | Author<br />
!style="width: 300px" | Remarks<br />
|-<br />
|Fin vs bulk<br />
|Timecourse microarray experiment using fin and bulk tissue<br />
|0, 1d, 3d<br />
|Mature tail: fin and bulk<br />
|Agilent, 44000<br />
|Fin_vs_bulk<br />
|Eugeniu Nacu<br />
|<br />
|-<br />
|Tail timecourse<br />
|Timecourse microarray experiment using tail<br />
|0, 3h, 6h, 12h, 18h, 24h, 36h, 48h, 72h, 120h, 168h, 288h<br />
|Mature tail<br />
|Agilent, 44000<br />
|Tail_timecourse<br />
|Eugeniu Nacu<br />
|<br />
|-<br />
|Limb timecourse<br />
|Timecourse microarray experiment using limb<br />
|0, 3h, 6h, 9h, 12h, 24h, 36h, 52h, 72h, 120h, 168h, 288h, 528h<br />
|Mature limb and limb bud<br />
|Agilent, 44000<br />
|Limb_timecourse<br />
|Dunja Knapp<br />
|<br />
|}</div>
Serghein
https://wiki.tanakalab.org/index.php?title=Datasets&diff=224
Datasets
2013-01-31T13:44:19Z
<p>Serghein: /* Illumina */</p>
<hr />
<div>== Sequences ==<br />
=== Illumina ===<br />
The data can be found under <b>//biodata/groups/crtd_tanaka/LabData/Sequencing/Illumina</b>.<br />
{| class="wikitable sortable"<br />
!style="width: 200px" class="unsortable" | Name<br />
!style="width: 300px" class="unsortable" | Description<br />
!style="width: 200px" | Tissue<br />
!style="width: 90px" class="unsortable" | Type<br />
!style="width: 80px" class="unsortable" | Read length<br />
!style="width: 100px" | Reads<br />
!style="width: 100px" class="unsortable" | Format<br />
!style="width: 200px" class="unsortable" | Location<br />
!style="width: 100px" | Author<br />
!style="width: 300px" class="unsortable" | Remarks<br />
|-<br />
|Mature spinal cord<br />
|Mature axolotl spinal cord<br />
|Spinal cord<br />
|Paired-ended<br />
|100bp<br />
|65,753,941<br />
|FastQ<br />
|SpinalCord/mSC.fastq.tar.gz<br />
|Akira Tazaki<br />
|<br />
|- <br />
|Injured spinal cord<br />
|Injured axolotl spinal cord, 6dpi<br />
|Spinal cord<br />
|Paired-ended<br />
|100bp<br />
|78,459,950<br />
|FastQ<br />
|SpinalCord/6diSC.fastq.tar.gz<br />
|Akira Tazaki<br />
|<br />
|-<br />
|Mature spinal cord<br />
|Mature axolotl spinal cord, replicate 2, crossing 142x5<br />
|Spinal cord<br />
|Paired-ended<br />
|100bp<br />
|101,769,559<br />
|FastQ<br />
|SpinalCord/mSC_142x5.fastq.tar.gz<br />
|Akira Tazaki<br />
|Due to a sequencer failure only the first 66 bases are safe<br />
|- <br />
|Mature spinal cord<br />
|Mature axolotl spinal cord, replicate 3, crossing 96x6<br />
|Spinal cord<br />
|Paired-ended<br />
|100bp<br />
|95,946,545<br />
|FastQ<br />
|SpinalCord/mSC_96x6.fastq.tar.gz<br />
|Akira Tazaki<br />
|Due to a sequencer failure only the first 66 bases are safe<br />
|- <br />
|Injured spinal cord<br />
|Injured axolotl spinal cord, 6dpi, replicate 2, crossing 142x5<br />
|Spinal cord<br />
|Paired-ended<br />
|100bp<br />
|96,626,387<br />
|FastQ<br />
|SpinalCord/6diSC_142x5.fastq.tar.gz<br />
|Akira Tazaki<br />
|Due to a sequencer failure only the first 66 bases are safe<br />
|- <br />
|Injured spinal cord<br />
|Injured axolotl spinal cord, 6dpi, replicate 3, crossing 96x5<br />
|Spinal cord<br />
|Paired-ended<br />
|100bp<br />
|99,855,603<br />
|FastQ<br />
|SpinalCord/6diSC_96x5.fastq.tar.gz<br />
|Akira Tazaki<br />
|Due to a sequencer failure only the first 66 bases are safe<br />
|-<br />
|Mature limb<br />
|Mature axolotl forelimb<br />
|Limb<br />
|Single-ended<br />
|76bp<br />
|65,934,228<br />
|FastQ<br />
|Limb/Mature.fastq.tar.gz<br />
|Dunja Knapp<br />
|<br />
|-<br />
|Amputated limb (36h)<br />
|Amputated axolotl forelimb (36hpa)<br />
|Limb<br />
|Single-ended<br />
|76bp<br />
|65,250,768<br />
|FastQ<br />
|Limb/36h_amp.fastq.tar.gz<br />
|Dunja Knapp<br />
|<br />
|-<br />
|Amputated limb (72h)<br />
|Amputated axolotl forelimb (72hpa)<br />
|Limb<br />
|Single-ended<br />
|76bp<br />
|62,970,898<br />
|FastQ<br />
|Limb/72h_amp.fastq.tar.gz<br />
|Dunja Knapp<br />
|<br />
|-<br />
|Lateral wound (36h)<br />
|Injured (lateral wound) axolotl forelimb (36hpw)<br />
|Limb<br />
|Single-ended<br />
|76bp<br />
|66,361,470<br />
|FastQ<br />
|Limb/36h_lw.fastq.tar.gz<br />
|Dunja Knapp<br />
|<br />
|-<br />
|Lateral wound (72h)<br />
|Injured (lateral wound) axolotl forelimb (72hpw)<br />
|Limb<br />
|Single-ended<br />
|76bp<br />
|64,133,834<br />
|FastQ<br />
|Limb/72h_lw.fastq.tar.gz<br />
|Dunja Knapp<br />
|<br />
|-<br />
|LPM-transplant<br />
|Blastema samples of a LPM-transplanted animal: mature and 1dpa<br />
|Blastema<br />
|Single-ended<br />
|<br />
|<br />
|FastQ<br />
|LPM/An3.fastq.tar.gz<br />
|Prayag Murawala/Dunja Knapp<br />
|GFP-labeled LPM was transplanted to a white-host embryo. The limb of the host was amputated and the blastema sample was collected.<br />
|-<br />
|LPM-transplant<br />
|Blastema samples of a LPM-transplanted animal: mature and 10dpa<br />
|Blastema<br />
|Single-ended<br />
|<br />
|<br />
|FastQ<br />
|LPM/An4.fastq.tar.gz<br />
|Prayag Murawala/Dunja Knapp<br />
|GFP-labeled LPM was transplanted to a white-host embryo. The limb of the host was amputated and the blastema sample was collected.<br />
|-<br />
|LPM-transplant<br />
|Blastema samples of a LPM-transplanted animal: mature and 5dpa<br />
|Blastema<br />
|Single-ended<br />
|<br />
|<br />
|FastQ<br />
|LPM/An6.fastq.tar.gz<br />
|Prayag Murawala/Dunja Knapp<br />
|GFP-labeled LPM was transplanted to a white-host embryo. The limb of the host was amputated and the blastema sample was collected.<br />
|-<br />
|LPM-transplant<br />
|Blastema samples of a LPM-transplanted animal: mature and 7dpa<br />
|Blastema<br />
|Single-ended<br />
|<br />
|<br />
|FastQ<br />
|LPM/An7.fastq.tar.gz<br />
|Prayag Murawala/Dunja Knapp<br />
|GFP-labeled LPM was transplanted to a white-host embryo. The limb of the host was amputated and the blastema sample was collected. <br />
|-<br />
|LPM-transplant<br />
|Blastema samples of a LPM-transplanted animal: mature and 3dpa<br />
|Blastema<br />
|Single-ended<br />
|<br />
|<br />
|FastQ<br />
|LPM/An8.fastq.tar.gz<br />
|Prayag Murawala/Dunja Knapp<br />
|GFP-labeled LPM was transplanted to a white-host embryo. The limb of the host was amputated and the blastema sample was collected.<br />
|}<br />
<br />
Unsorted Illumina data can be found under <b>//biodata/groups/crtd_tanaka/LabData/Sequencing/Illumina</b>.<br />
<br />
=== Sanger ===<br />
The data can be found under <b>//biodata/groups/crtd_tanaka/LabData/Sequencing/Sanger</b>.<br />
{| class="wikitable sortable"<br />
!style="width: 200px" class="unsortable" | Name<br />
!style="width: 300px" class="unsortable" | Description<br />
!style="width: 200px" | Tissue<br />
!style="width: 200px" | Sequences<br />
!style="width: 300px" class="unsortable" | Location<br />
!style="width: 100px" | Author<br />
!style="width: 300px" class="unsortable" | Remarks<br />
|-<br />
|LimbBlastema<br />
|Limb blastema library<br />
|Limb blastema<br />
|20160 (RSD) / 15648 (SCF)<br />
|<ul><li>SCF files: LimbBlastema/LB_SCF.gz</li><li>RSD files: LimbBlastema/LB_RSD.gz</li></ul><br />
|Akira Tazaki<br />
|<br />
|-<br />
|NeuraTube<br />
|Neural tube library<br />
|Teural tube<br />
|4896 (RSD) / 7905 (SCF)<br />
|<ul><li>SCF files: NeuralTube/NT_SCF.gz</li><li>RSD files: NeuralTube/NT_RSD.gz</li></ul><br />
|Akira Tazaki<br />
|<br />
|}<br />
<br />
=== Roche/454 ===<br />
The data can be found under <b>//biodata/groups/crtd_tanaka/LabData/Sequencing/454</b>.<br />
{| class="wikitable"<br />
!style="width: 200px" | Name<br />
!style="width: 300px" | Description<br />
!style="width: 200px" | Tissue<br />
!style="width: 200px" | Reads<br />
!style="width: 200px" | Format<br />
!style="width: 300px" | Location<br />
!style="width: 100px" | Author<br />
!style="width: 300px" | Remarks<br />
|-<br />
|454<br />
|Mixed 454<br />
|Mixed<br />
|1,208,954<br />
|Fasta/Qual<br />
|Ax_454.tar.gz<br />
|n/a<br />
|}<br />
<br />
== Microarrays ==<br />
The data can be found under <b>//biodata/groups/crtd_tanaka/LabData/Microarrays</b>. Also consult the file <b>Contents.txt</b> in the experiment directory for more details. The raw data (*.tiff) files can be found in the subdirectory <b>Raw</b> in the experiment directory.<br />
{| class="wikitable"<br />
!style="width: 200px" | Name<br />
!style="width: 300px" | Description<br />
!style="width: 300px" | Timepoints<br />
!style="width: 200px" | Tissue<br />
!style="width: 110px" | Array type<br />
!style="width: 250px" | Location<br />
!style="width: 100px" | Author<br />
!style="width: 300px" | Remarks<br />
|-<br />
|Fin vs bulk<br />
|Timecourse microarray experiment using fin and bulk tissue<br />
|0, 1d, 3d<br />
|Mature tail: fin and bulk<br />
|Agilent, 44000<br />
|Fin_vs_bulk<br />
|Eugeniu Nacu<br />
|<br />
|-<br />
|Tail timecourse<br />
|Timecourse microarray experiment using tail<br />
|0, 3h, 6h, 12h, 18h, 24h, 36h, 48h, 72h, 120h, 168h, 288h<br />
|Mature tail<br />
|Agilent, 44000<br />
|Tail_timecourse<br />
|Eugeniu Nacu<br />
|<br />
|-<br />
|Limb timecourse<br />
|Timecourse microarray experiment using limb<br />
|0, 3h, 6h, 9h, 12h, 24h, 36h, 52h, 72h, 120h, 168h, 288h, 528h<br />
|Mature limb and limb bud<br />
|Agilent, 44000<br />
|Limb_timecourse<br />
|Dunja Knapp<br />
|<br />
|}</div>
Serghein
https://wiki.tanakalab.org/index.php?title=Datasets&diff=223
Datasets
2013-01-30T12:58:17Z
<p>Serghein: /* Microarrays */</p>
<hr />
<div>== Sequences ==<br />
=== Illumina ===<br />
The data can be found under <b>//biodata/groups/crtd_tanaka/LabData/Sequencing/Illumina</b>.<br />
{| class="wikitable sortable"<br />
!style="width: 200px" class="unsortable" | Name<br />
!style="width: 300px" class="unsortable" | Description<br />
!style="width: 200px" | Tissue<br />
!style="width: 90px" class="unsortable" | Type<br />
!style="width: 80px" class="unsortable" | Read length<br />
!style="width: 100px" | Reads<br />
!style="width: 100px" class="unsortable" | Format<br />
!style="width: 200px" class="unsortable" | Location<br />
!style="width: 100px" | Author<br />
!style="width: 300px" class="unsortable" | Remarks<br />
|-<br />
|Mature spinal cord<br />
|Mature axolotl spinal cord<br />
|Spinal cord<br />
|Paired-ended<br />
|100bp<br />
|65,753,941<br />
|FastQ<br />
|SpinalCord/mSC.fastq.tar.gz<br />
|Akira Tazaki<br />
|<br />
|- <br />
|Injured spinal cord<br />
|Injured axolotl spinal cord, 6dpi<br />
|Spinal cord<br />
|Paired-ended<br />
|100bp<br />
|78,459,950<br />
|FastQ<br />
|SpinalCord/6diSC.fastq.tar.gz<br />
|Akira Tazaki<br />
|<br />
|-<br />
|Mature spinal cord<br />
|Mature axolotl spinal cord, replicate 2, crossing 142x5<br />
|Spinal cord<br />
|Paired-ended<br />
|100bp<br />
|101,769,559<br />
|FastQ<br />
|SpinalCord/mSC_142x5.fastq.tar.gz<br />
|Akira Tazaki<br />
|Due to a sequencer failure only the first 66 bases are safe<br />
|- <br />
|Mature spinal cord<br />
|Mature axolotl spinal cord, replicate 3, crossing 96x6<br />
|Spinal cord<br />
|Paired-ended<br />
|100bp<br />
|95,946,545<br />
|FastQ<br />
|SpinalCord/mSC_96x6.fastq.tar.gz<br />
|Akira Tazaki<br />
|Due to a sequencer failure only the first 66 bases are safe<br />
|- <br />
|Injured spinal cord<br />
|Injured axolotl spinal cord, 6dpi, replicate 2, crossing 142x5<br />
|Spinal cord<br />
|Paired-ended<br />
|100bp<br />
|96,626,387<br />
|FastQ<br />
|SpinalCord/6diSC_142x5.fastq.tar.gz<br />
|Akira Tazaki<br />
|Due to a sequencer failure only the first 66 bases are safe<br />
|- <br />
|Injured spinal cord<br />
|Injured axolotl spinal cord, 6dpi, replicate 3, crossing 96x5<br />
|Spinal cord<br />
|Paired-ended<br />
|100bp<br />
|99,855,603<br />
|FastQ<br />
|SpinalCord/6diSC_96x5.fastq.tar.gz<br />
|Akira Tazaki<br />
|Due to a sequencer failure only the first 66 bases are safe<br />
|-<br />
|Mature limb<br />
|Mature axolotl forelimb<br />
|Limb<br />
|Single-ended<br />
|76bp<br />
|65,934,228<br />
|FastQ<br />
|Limb/Mature.fastq.tar.gz<br />
|Dunja Knapp<br />
|<br />
|-<br />
|Amputated limb (36h)<br />
|Amputated axolotl forelimb (36hpa)<br />
|Limb<br />
|Single-ended<br />
|76bp<br />
|65,250,768<br />
|FastQ<br />
|Limb/36h_amp.fastq.tar.gz<br />
|Dunja Knapp<br />
|<br />
|-<br />
|Amputated limb (72h)<br />
|Amputated axolotl forelimb (72hpa)<br />
|Limb<br />
|Single-ended<br />
|76bp<br />
|62,970,898<br />
|FastQ<br />
|Limb/72h_amp.fastq.tar.gz<br />
|Dunja Knapp<br />
|<br />
|-<br />
|Lateral wound (36h)<br />
|Injured (lateral wound) axolotl forelimb (36hpw)<br />
|Limb<br />
|Single-ended<br />
|76bp<br />
|66,361,470<br />
|FastQ<br />
|Limb/36h_lw.fastq.tar.gz<br />
|Dunja Knapp<br />
|<br />
|-<br />
|Lateral wound (72h)<br />
|Injured (lateral wound) axolotl forelimb (72hpw)<br />
|Limb<br />
|Single-ended<br />
|76bp<br />
|64,133,834<br />
|FastQ<br />
|Limb/72h_lw.fastq.tar.gz<br />
|Dunja Knapp<br />
|<br />
|}<br />
<br />
Unsorted Illumina data can be found under <b>//biodata/groups/crtd_tanaka/LabData/Sequencing/Illumina</b>.<br />
<br />
=== Sanger ===<br />
The data can be found under <b>//biodata/groups/crtd_tanaka/LabData/Sequencing/Sanger</b>.<br />
{| class="wikitable sortable"<br />
!style="width: 200px" class="unsortable" | Name<br />
!style="width: 300px" class="unsortable" | Description<br />
!style="width: 200px" | Tissue<br />
!style="width: 200px" | Sequences<br />
!style="width: 300px" class="unsortable" | Location<br />
!style="width: 100px" | Author<br />
!style="width: 300px" class="unsortable" | Remarks<br />
|-<br />
|LimbBlastema<br />
|Limb blastema library<br />
|Limb blastema<br />
|20160 (RSD) / 15648 (SCF)<br />
|<ul><li>SCF files: LimbBlastema/LB_SCF.gz</li><li>RSD files: LimbBlastema/LB_RSD.gz</li></ul><br />
|Akira Tazaki<br />
|<br />
|-<br />
|NeuraTube<br />
|Neural tube library<br />
|Teural tube<br />
|4896 (RSD) / 7905 (SCF)<br />
|<ul><li>SCF files: NeuralTube/NT_SCF.gz</li><li>RSD files: NeuralTube/NT_RSD.gz</li></ul><br />
|Akira Tazaki<br />
|<br />
|}<br />
<br />
=== Roche/454 ===<br />
The data can be found under <b>//biodata/groups/crtd_tanaka/LabData/Sequencing/454</b>.<br />
{| class="wikitable"<br />
!style="width: 200px" | Name<br />
!style="width: 300px" | Description<br />
!style="width: 200px" | Tissue<br />
!style="width: 200px" | Reads<br />
!style="width: 200px" | Format<br />
!style="width: 300px" | Location<br />
!style="width: 100px" | Author<br />
!style="width: 300px" | Remarks<br />
|-<br />
|454<br />
|Mixed 454<br />
|Mixed<br />
|1,208,954<br />
|Fasta/Qual<br />
|Ax_454.tar.gz<br />
|n/a<br />
|}<br />
<br />
== Microarrays ==<br />
The data can be found under <b>//biodata/groups/crtd_tanaka/LabData/Microarrays</b>. Also consult the file <b>Contents.txt</b> in the experiment directory for more details. The raw data (*.tiff) files can be found in the subdirectory <b>Raw</b> in the experiment directory.<br />
{| class="wikitable"<br />
!style="width: 200px" | Name<br />
!style="width: 300px" | Description<br />
!style="width: 300px" | Timepoints<br />
!style="width: 200px" | Tissue<br />
!style="width: 110px" | Array type<br />
!style="width: 250px" | Location<br />
!style="width: 100px" | Author<br />
!style="width: 300px" | Remarks<br />
|-<br />
|Fin vs bulk<br />
|Timecourse microarray experiment using fin and bulk tissue<br />
|0, 1d, 3d<br />
|Mature tail: fin and bulk<br />
|Agilent, 44000<br />
|Fin_vs_bulk<br />
|Eugeniu Nacu<br />
|<br />
|-<br />
|Tail timecourse<br />
|Timecourse microarray experiment using tail<br />
|0, 3h, 6h, 12h, 18h, 24h, 36h, 48h, 72h, 120h, 168h, 288h<br />
|Mature tail<br />
|Agilent, 44000<br />
|Tail_timecourse<br />
|Eugeniu Nacu<br />
|<br />
|-<br />
|Limb timecourse<br />
|Timecourse microarray experiment using limb<br />
|0, 3h, 6h, 9h, 12h, 24h, 36h, 52h, 72h, 120h, 168h, 288h, 528h<br />
|Mature limb and limb bud<br />
|Agilent, 44000<br />
|Limb_timecourse<br />
|Dunja Knapp<br />
|<br />
|}</div>
Serghein
https://wiki.tanakalab.org/index.php?title=Overview&diff=222
Overview
2013-01-29T16:28:16Z
<p>Serghein: /* Lab life */</p>
<hr />
<div>== Introduction ==<br />
On the pages listed below you can find most common protocols used in the lab as well as a list of lab duties along with the names of the responsible persons. Please, contact the responsible persons if you have any question, suggestions or troubles.<br />
<br />
== Axolotl ==<br />
<ul><br />
<li>[[Axolotl#Maintaining_the_axolotls|Maintainance]]</li><br />
<li>[[Axolotl#Feeding|Feeding]]</li><br />
</ul><br />
<br />
== Lab duties ==<br />
<ul><br />
=== Chemicals ===<br />
<li>[[Antibiotics|Antibiotics]]</li><br />
<li>[[Benzocaine|Benzocaine]]</li><br />
<li>[[Fibronectin|Fibronectin]]</li><br />
<li>[[Gelatine|Gelatine]]</li><br />
<li>[[Liquid_nitrogen|Liquid nitrogen]]</li><br />
<li>[[Primary_antibodies|Primary antibodies]]</li><br />
<li>[[Secondary_antibodies|Secondary antibodies]]</li><br />
<li>[[Serum_immunostaining|Serum immunostaining]]</li><br />
<br />
=== Hardware ===<br />
<li>[[Autoclave|Autoclave]]</li><br />
<li>[[Cryostat|Cryostat]]</li><br />
<li>[[Dissecting_microscopes|Dissecting microscopes]]</li><br />
<li>[[Leica_confocal_microscope|Leica confocal microscope]]</li><br />
<li>[[Vacuum_pumps|Vacuum pumps]]</li><br />
<li>[[Waterbath|Waterbath]]</li><br />
<br />
=== General ===<br />
<li>[[Ordering_common_stuff|Ordering common stuff]]</li><br />
<li>[[Heat_shock_competent_cells|Heat-shock competent cells]]</li><br />
</ul><br />
<br />
<br />
== Protocols ==<br />
<ul><br />
=== Cell culture ===<br />
<li>[[Blastema_cells|Blastema cells]]</li><br />
<li>[[Baculovirus_titration|Baculovirus titration]]</li><br />
<li>[[Myoblasts_electroporation|Myoblasts electroporation]]</li><br />
<li>[[Adhesive_cell_culture|Adhesive cell culture]]</li><br />
<li>[[Electroporation_of_blastema_cells|Electroporation of blastema cells]]</li><br />
<li>[[Electroporation_of_nec|Electroporation of neural epithelia cells (axolotl spinal cord)]]</li><br />
<li>[[mESC_culture|mESC culture/Cyst formation]]</li><br />
<li>[[Neurosphere_culture|Neurosphere culture]]</li><br />
=== Histology ===<br />
=== Molecular biology ===<br />
</ul><br />
<br />
<br />
== Booking calendars ==<br />
Since some pieces of hardware are used intensively it is necessary to book them in advance. The links to the corresponding booking calendars are listed below.<br />
<ul><br />
<li><br />
Fluorescence microscopes<br />
<ul><br />
<li>[http://www.my.calendars.net/olympusszx16 Olympus SZX 16]</li><br />
<li>[http://www.my.calendars.net/new_olympus/ New Olympus SZX 16]</li><br />
<li>[http://www.my.calendars.net/Olympus_OVK Olympus OVK]</li><br />
<li>[http://www.my.calendars.net/axio_observer/ Axio Observer]</li><br />
</ul><br />
</li><br />
<li><br />
Microinjectors and electroporators<br />
<ul><br />
<li>[http://www.my.calendars.net/electroporator Electroporator]</li><br />
<li>[http://www.my.calendars.net/electroporator2 2nd electroporator]</li><br />
<li>[http://www.my.calendars.net/microinjector Microinjector]</li><br />
<li>[http://www.my.calendars.net/stereoscope2/d01/11/2012 Stereoscope]</li><br />
</ul><br />
</li><br />
<li><br />
Confocal microscopes<br />
<ul><br />
<li>[http://www.my.calendars.net/leica_lsm Leica LSM]</li><br />
</ul><br />
</li><br />
<li><br />
Cryostats<br />
<ul><br />
<li>[http://www.my.calendars.net/cryostat1 Cryostat 1]</li><br />
<li>[http://www.my.calendars.net/cryostat2 Cryostat 2]</li><br />
</ul><br />
</li><br />
<li><br />
Microtome<br />
<ul><br />
<li>[http://www.my.calendars.net/microtome Microtome]</li><br />
</ul><br />
</li><br />
</ul><br />
<br />
== Transgenic lines ==<br />
<ul><br />
<li>[[Transgenic_axolotl_lines|Axolotl (A.mexicanum)]]</li><br />
<li>[[Transgenic_frog_lines|Frog (X.laevis)]]</li><br />
</ul><br />
<br />
== Digital data ==<br />
Over the years the members of the lab have produced a lot of different data: Sanger sequences, EST libraries, images and so on. <br />
Select a category from the list below in order to view or download the data.<br />
<br />
=== Fileservers ===<br />
{| class="wikitable"<br />
!style="width: 350px" | Location<br />
!style="width: 250px" | Volume size<br />
!style="width: 350px" | Description<br />
!style="width: 350px" | Access<br />
!style="width: 350px" | Location (console only)<br />
|-<br />
|//biodata/groups/<b>crtd_tanaka</b><br />
|16 TB<br />
|General purpose storage space<br />
|Entire Tanaka lab<br />
|<i>biocluster:</i> <b>/group/crtd_tanaka</b><br />
|-<br />
|//biodata/groups/<b>tanaka-ests</b><br />
|247 GB<br />
|EST sequences<br />
|Entire Tanaka lab<br />
|<i>biocluster:</i> <b>/group/tanaka-ests</b><br />
|-<br />
|//biodata/groups/<b>axolotl-transcriptome</b><br />
|117 GB<br />
|Axolotl transcriptome data<br />
|Elly, Sergej<br />
|<i>biocluster:</i> <b>/projects/axolotl-transcriptome</b><br />
|-<br />
|//biodata/groups/<b>tanaka-saori</b><br />
|878 GB<br />
|Special directory for Saori's data<br />
|Elly, Saori, Sergej<br />
|<i>biocluster:</i> <b>/group/tanaka-saori</b><br />
|}<br />
<br />
{{Tip|The path is different, when accessing the file server from the console.}}<br />
<br />
=== Literature ===<br />
<ul><br />
<li>[[Literature#Theses|Theses]]</li><br />
<li>[[Literature#Publications|Publications]]</li><br />
</ul><br />
<br />
=== Databases ===<br />
<ul><br />
<li>[https://python-srv1.mpi-cbg.de/axolotl/cgi-bin/login.cgi Axolotl EST] database contains several ESTs and also some additional information, e.g. the position of the well with the corresponding insert in the Blastema (BL) or Neural tube (NT) library.</li><br />
<li>[http://est.age.mpg.de/cgi-bin/result.py Axologle] database contains several different Axolotl transciptome assemblies</li><br />
</ul><br />
<br />
=== Datasets ===<br />
<ul><br />
<li>[[Datasets#Sequences|Sequences]]<br />
<ul><br />
<li>[[Datasets#Illumina|Illumina]]</li><br />
<li>[[Datasets#Sanger|Sanger]]</li><br />
<li>[[Datasets#Roche.2F454|Roche/454]]</li><br />
</ul><br />
</li><br />
<li>[[Datasets#Microarrays|Microarrays]]<br />
</ul><br />
<br />
== Lab life ==<br />
<ul><br />
<li>[[Lab_photos|Lab photos]]</li><br />
<li>Further pictures can be found in <b>/biodata/groups/crtd_tanaka/LabFun/</b></li><br />
<li>The recepies for Heino's farewell present can be found under <b>/biodata/groups/crtd_tanaka/LabFun/Heino's farewell present/</b></li><br />
<li>The video of the visit of the EU commissioner can be found under <b>/biodata/groups/crtd_tanaka/LabFun/</b></li><br />
</ul></div>
Serghein
https://wiki.tanakalab.org/index.php?title=Overview&diff=221
Overview
2013-01-29T16:26:24Z
<p>Serghein: /* Lab life */</p>
<hr />
<div>== Introduction ==<br />
On the pages listed below you can find most common protocols used in the lab as well as a list of lab duties along with the names of the responsible persons. Please, contact the responsible persons if you have any question, suggestions or troubles.<br />
<br />
== Axolotl ==<br />
<ul><br />
<li>[[Axolotl#Maintaining_the_axolotls|Maintainance]]</li><br />
<li>[[Axolotl#Feeding|Feeding]]</li><br />
</ul><br />
<br />
== Lab duties ==<br />
<ul><br />
=== Chemicals ===<br />
<li>[[Antibiotics|Antibiotics]]</li><br />
<li>[[Benzocaine|Benzocaine]]</li><br />
<li>[[Fibronectin|Fibronectin]]</li><br />
<li>[[Gelatine|Gelatine]]</li><br />
<li>[[Liquid_nitrogen|Liquid nitrogen]]</li><br />
<li>[[Primary_antibodies|Primary antibodies]]</li><br />
<li>[[Secondary_antibodies|Secondary antibodies]]</li><br />
<li>[[Serum_immunostaining|Serum immunostaining]]</li><br />
<br />
=== Hardware ===<br />
<li>[[Autoclave|Autoclave]]</li><br />
<li>[[Cryostat|Cryostat]]</li><br />
<li>[[Dissecting_microscopes|Dissecting microscopes]]</li><br />
<li>[[Leica_confocal_microscope|Leica confocal microscope]]</li><br />
<li>[[Vacuum_pumps|Vacuum pumps]]</li><br />
<li>[[Waterbath|Waterbath]]</li><br />
<br />
=== General ===<br />
<li>[[Ordering_common_stuff|Ordering common stuff]]</li><br />
<li>[[Heat_shock_competent_cells|Heat-shock competent cells]]</li><br />
</ul><br />
<br />
<br />
== Protocols ==<br />
<ul><br />
=== Cell culture ===<br />
<li>[[Blastema_cells|Blastema cells]]</li><br />
<li>[[Baculovirus_titration|Baculovirus titration]]</li><br />
<li>[[Myoblasts_electroporation|Myoblasts electroporation]]</li><br />
<li>[[Adhesive_cell_culture|Adhesive cell culture]]</li><br />
<li>[[Electroporation_of_blastema_cells|Electroporation of blastema cells]]</li><br />
<li>[[Electroporation_of_nec|Electroporation of neural epithelia cells (axolotl spinal cord)]]</li><br />
<li>[[mESC_culture|mESC culture/Cyst formation]]</li><br />
<li>[[Neurosphere_culture|Neurosphere culture]]</li><br />
=== Histology ===<br />
=== Molecular biology ===<br />
</ul><br />
<br />
<br />
== Booking calendars ==<br />
Since some pieces of hardware are used intensively it is necessary to book them in advance. The links to the corresponding booking calendars are listed below.<br />
<ul><br />
<li><br />
Fluorescence microscopes<br />
<ul><br />
<li>[http://www.my.calendars.net/olympusszx16 Olympus SZX 16]</li><br />
<li>[http://www.my.calendars.net/new_olympus/ New Olympus SZX 16]</li><br />
<li>[http://www.my.calendars.net/Olympus_OVK Olympus OVK]</li><br />
<li>[http://www.my.calendars.net/axio_observer/ Axio Observer]</li><br />
</ul><br />
</li><br />
<li><br />
Microinjectors and electroporators<br />
<ul><br />
<li>[http://www.my.calendars.net/electroporator Electroporator]</li><br />
<li>[http://www.my.calendars.net/electroporator2 2nd electroporator]</li><br />
<li>[http://www.my.calendars.net/microinjector Microinjector]</li><br />
<li>[http://www.my.calendars.net/stereoscope2/d01/11/2012 Stereoscope]</li><br />
</ul><br />
</li><br />
<li><br />
Confocal microscopes<br />
<ul><br />
<li>[http://www.my.calendars.net/leica_lsm Leica LSM]</li><br />
</ul><br />
</li><br />
<li><br />
Cryostats<br />
<ul><br />
<li>[http://www.my.calendars.net/cryostat1 Cryostat 1]</li><br />
<li>[http://www.my.calendars.net/cryostat2 Cryostat 2]</li><br />
</ul><br />
</li><br />
<li><br />
Microtome<br />
<ul><br />
<li>[http://www.my.calendars.net/microtome Microtome]</li><br />
</ul><br />
</li><br />
</ul><br />
<br />
== Transgenic lines ==<br />
<ul><br />
<li>[[Transgenic_axolotl_lines|Axolotl (A.mexicanum)]]</li><br />
<li>[[Transgenic_frog_lines|Frog (X.laevis)]]</li><br />
</ul><br />
<br />
== Digital data ==<br />
Over the years the members of the lab have produced a lot of different data: Sanger sequences, EST libraries, images and so on. <br />
Select a category from the list below in order to view or download the data.<br />
<br />
=== Fileservers ===<br />
{| class="wikitable"<br />
!style="width: 350px" | Location<br />
!style="width: 250px" | Volume size<br />
!style="width: 350px" | Description<br />
!style="width: 350px" | Access<br />
!style="width: 350px" | Location (console only)<br />
|-<br />
|//biodata/groups/<b>crtd_tanaka</b><br />
|16 TB<br />
|General purpose storage space<br />
|Entire Tanaka lab<br />
|<i>biocluster:</i> <b>/group/crtd_tanaka</b><br />
|-<br />
|//biodata/groups/<b>tanaka-ests</b><br />
|247 GB<br />
|EST sequences<br />
|Entire Tanaka lab<br />
|<i>biocluster:</i> <b>/group/tanaka-ests</b><br />
|-<br />
|//biodata/groups/<b>axolotl-transcriptome</b><br />
|117 GB<br />
|Axolotl transcriptome data<br />
|Elly, Sergej<br />
|<i>biocluster:</i> <b>/projects/axolotl-transcriptome</b><br />
|-<br />
|//biodata/groups/<b>tanaka-saori</b><br />
|878 GB<br />
|Special directory for Saori's data<br />
|Elly, Saori, Sergej<br />
|<i>biocluster:</i> <b>/group/tanaka-saori</b><br />
|}<br />
<br />
{{Tip|The path is different, when accessing the file server from the console.}}<br />
<br />
=== Literature ===<br />
<ul><br />
<li>[[Literature#Theses|Theses]]</li><br />
<li>[[Literature#Publications|Publications]]</li><br />
</ul><br />
<br />
=== Databases ===<br />
<ul><br />
<li>[https://python-srv1.mpi-cbg.de/axolotl/cgi-bin/login.cgi Axolotl EST] database contains several ESTs and also some additional information, e.g. the position of the well with the corresponding insert in the Blastema (BL) or Neural tube (NT) library.</li><br />
<li>[http://est.age.mpg.de/cgi-bin/result.py Axologle] database contains several different Axolotl transciptome assemblies</li><br />
</ul><br />
<br />
=== Datasets ===<br />
<ul><br />
<li>[[Datasets#Sequences|Sequences]]<br />
<ul><br />
<li>[[Datasets#Illumina|Illumina]]</li><br />
<li>[[Datasets#Sanger|Sanger]]</li><br />
<li>[[Datasets#Roche.2F454|Roche/454]]</li><br />
</ul><br />
</li><br />
<li>[[Datasets#Microarrays|Microarrays]]<br />
</ul><br />
<br />
== Lab life ==<br />
<ul><br />
<li>[[Lab_photos|Lab photos]]</li><br />
<li>Further pictures can be found in <b>/biodata/groups/crtd_tanaka/Lab Fun/</b></li><br />
<li>The recepies for Heino's farewell present can be found under <b>/biodata/groups/crtd_tanaka/Lab Fun/Heino's farewell present/</b></li><br />
<li>The video of the visit of the EU commissioner can be found under <b>/biodata/groups/crtd_tanaka/Lab Fun/</b></li><br />
</ul></div>
Serghein
https://wiki.tanakalab.org/index.php?title=Overview&diff=220
Overview
2013-01-29T16:06:25Z
<p>Serghein: /* Fileservers */</p>
<hr />
<div>== Introduction ==<br />
On the pages listed below you can find most common protocols used in the lab as well as a list of lab duties along with the names of the responsible persons. Please, contact the responsible persons if you have any question, suggestions or troubles.<br />
<br />
== Axolotl ==<br />
<ul><br />
<li>[[Axolotl#Maintaining_the_axolotls|Maintainance]]</li><br />
<li>[[Axolotl#Feeding|Feeding]]</li><br />
</ul><br />
<br />
== Lab duties ==<br />
<ul><br />
=== Chemicals ===<br />
<li>[[Antibiotics|Antibiotics]]</li><br />
<li>[[Benzocaine|Benzocaine]]</li><br />
<li>[[Fibronectin|Fibronectin]]</li><br />
<li>[[Gelatine|Gelatine]]</li><br />
<li>[[Liquid_nitrogen|Liquid nitrogen]]</li><br />
<li>[[Primary_antibodies|Primary antibodies]]</li><br />
<li>[[Secondary_antibodies|Secondary antibodies]]</li><br />
<li>[[Serum_immunostaining|Serum immunostaining]]</li><br />
<br />
=== Hardware ===<br />
<li>[[Autoclave|Autoclave]]</li><br />
<li>[[Cryostat|Cryostat]]</li><br />
<li>[[Dissecting_microscopes|Dissecting microscopes]]</li><br />
<li>[[Leica_confocal_microscope|Leica confocal microscope]]</li><br />
<li>[[Vacuum_pumps|Vacuum pumps]]</li><br />
<li>[[Waterbath|Waterbath]]</li><br />
<br />
=== General ===<br />
<li>[[Ordering_common_stuff|Ordering common stuff]]</li><br />
<li>[[Heat_shock_competent_cells|Heat-shock competent cells]]</li><br />
</ul><br />
<br />
<br />
== Protocols ==<br />
<ul><br />
=== Cell culture ===<br />
<li>[[Blastema_cells|Blastema cells]]</li><br />
<li>[[Baculovirus_titration|Baculovirus titration]]</li><br />
<li>[[Myoblasts_electroporation|Myoblasts electroporation]]</li><br />
<li>[[Adhesive_cell_culture|Adhesive cell culture]]</li><br />
<li>[[Electroporation_of_blastema_cells|Electroporation of blastema cells]]</li><br />
<li>[[Electroporation_of_nec|Electroporation of neural epithelia cells (axolotl spinal cord)]]</li><br />
<li>[[mESC_culture|mESC culture/Cyst formation]]</li><br />
<li>[[Neurosphere_culture|Neurosphere culture]]</li><br />
=== Histology ===<br />
=== Molecular biology ===<br />
</ul><br />
<br />
<br />
== Booking calendars ==<br />
Since some pieces of hardware are used intensively it is necessary to book them in advance. The links to the corresponding booking calendars are listed below.<br />
<ul><br />
<li><br />
Fluorescence microscopes<br />
<ul><br />
<li>[http://www.my.calendars.net/olympusszx16 Olympus SZX 16]</li><br />
<li>[http://www.my.calendars.net/new_olympus/ New Olympus SZX 16]</li><br />
<li>[http://www.my.calendars.net/Olympus_OVK Olympus OVK]</li><br />
<li>[http://www.my.calendars.net/axio_observer/ Axio Observer]</li><br />
</ul><br />
</li><br />
<li><br />
Microinjectors and electroporators<br />
<ul><br />
<li>[http://www.my.calendars.net/electroporator Electroporator]</li><br />
<li>[http://www.my.calendars.net/electroporator2 2nd electroporator]</li><br />
<li>[http://www.my.calendars.net/microinjector Microinjector]</li><br />
<li>[http://www.my.calendars.net/stereoscope2/d01/11/2012 Stereoscope]</li><br />
</ul><br />
</li><br />
<li><br />
Confocal microscopes<br />
<ul><br />
<li>[http://www.my.calendars.net/leica_lsm Leica LSM]</li><br />
</ul><br />
</li><br />
<li><br />
Cryostats<br />
<ul><br />
<li>[http://www.my.calendars.net/cryostat1 Cryostat 1]</li><br />
<li>[http://www.my.calendars.net/cryostat2 Cryostat 2]</li><br />
</ul><br />
</li><br />
<li><br />
Microtome<br />
<ul><br />
<li>[http://www.my.calendars.net/microtome Microtome]</li><br />
</ul><br />
</li><br />
</ul><br />
<br />
== Transgenic lines ==<br />
<ul><br />
<li>[[Transgenic_axolotl_lines|Axolotl (A.mexicanum)]]</li><br />
<li>[[Transgenic_frog_lines|Frog (X.laevis)]]</li><br />
</ul><br />
<br />
== Digital data ==<br />
Over the years the members of the lab have produced a lot of different data: Sanger sequences, EST libraries, images and so on. <br />
Select a category from the list below in order to view or download the data.<br />
<br />
=== Fileservers ===<br />
{| class="wikitable"<br />
!style="width: 350px" | Location<br />
!style="width: 250px" | Volume size<br />
!style="width: 350px" | Description<br />
!style="width: 350px" | Access<br />
!style="width: 350px" | Location (console only)<br />
|-<br />
|//biodata/groups/<b>crtd_tanaka</b><br />
|16 TB<br />
|General purpose storage space<br />
|Entire Tanaka lab<br />
|<i>biocluster:</i> <b>/group/crtd_tanaka</b><br />
|-<br />
|//biodata/groups/<b>tanaka-ests</b><br />
|247 GB<br />
|EST sequences<br />
|Entire Tanaka lab<br />
|<i>biocluster:</i> <b>/group/tanaka-ests</b><br />
|-<br />
|//biodata/groups/<b>axolotl-transcriptome</b><br />
|117 GB<br />
|Axolotl transcriptome data<br />
|Elly, Sergej<br />
|<i>biocluster:</i> <b>/projects/axolotl-transcriptome</b><br />
|-<br />
|//biodata/groups/<b>tanaka-saori</b><br />
|878 GB<br />
|Special directory for Saori's data<br />
|Elly, Saori, Sergej<br />
|<i>biocluster:</i> <b>/group/tanaka-saori</b><br />
|}<br />
<br />
{{Tip|The path is different, when accessing the file server from the console.}}<br />
<br />
=== Literature ===<br />
<ul><br />
<li>[[Literature#Theses|Theses]]</li><br />
<li>[[Literature#Publications|Publications]]</li><br />
</ul><br />
<br />
=== Databases ===<br />
<ul><br />
<li>[https://python-srv1.mpi-cbg.de/axolotl/cgi-bin/login.cgi Axolotl EST] database contains several ESTs and also some additional information, e.g. the position of the well with the corresponding insert in the Blastema (BL) or Neural tube (NT) library.</li><br />
<li>[http://est.age.mpg.de/cgi-bin/result.py Axologle] database contains several different Axolotl transciptome assemblies</li><br />
</ul><br />
<br />
=== Datasets ===<br />
<ul><br />
<li>[[Datasets#Sequences|Sequences]]<br />
<ul><br />
<li>[[Datasets#Illumina|Illumina]]</li><br />
<li>[[Datasets#Sanger|Sanger]]</li><br />
<li>[[Datasets#Roche.2F454|Roche/454]]</li><br />
</ul><br />
</li><br />
<li>[[Datasets#Microarrays|Microarrays]]<br />
</ul><br />
<br />
== Lab life ==<br />
<ul><br />
<li>[[Lab_photos|Lab photos]]</li><br />
<li>Further pictures can be found in <b>/biodata/groups/crtd_tanaka/Lab Fun/</b><br />
<ul><br />
<li>Heino's farewell</li><br />
<li>Snow axolotl and snowball fight</li><br />
<li>Yu and Saori's farewell</li><br />
<li>Visit of Kathleen/Fabian and Laura/Mathilda</li><br />
</ul><br />
</li><br />
<li>The recepies for Heino's farewell present can be found under <b>/biodata/groups/crtd_tanaka/Lab Fun/Heino's farewell present/</b></li><br />
<li>The video of the visit of the EU commissioner can be found under <b>/biodata/groups/crtd_tanaka/Lab Fun/</b></li><br />
</ul></div>
Serghein