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== Introduction ==
== Introduction ==
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.
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.
== Axolotl ==
=== Maintaining the axolotls ===
=== Feeding ===
==== Artemia (Brine shrimp eggs) ====
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.
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.
===== Artemia Hatching Preparation: Protocol for 15 Ltr. =====
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 ☺
Add 50-60 ml full of dried artemia (Stored at 40C) to this.
===== Hatching preparation =====
* The following protocol is considered for 15 l solution.
* Switch on the bubbler.
* 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.
* Switch on the heating. And make sure that the light on the top is on.
* Add 50-60 ml full of dried artemia (Stored at 40C) to this.
Keep it like this for 2 days with aeration. And >200 Lux of light.<br />
Usually they hatch within few hours but It is good to keep for 2 days to achieve a good hatching.<br />
During these two days temperature can be 18°-20°C.<br />
Make sure hatching container is not getting clogged during these two days.<br />


== Lab duties ==
== Lab duties ==
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<li>[[Fibronectin|Fibronectin]]</li>
<li>[[Fibronectin|Fibronectin]]</li>
<li>[[Gelatine|Gelatine]]</li>
<li>[[Gelatine|Gelatine]]</li>
<li>[[Liquid nitrogen|Liquid nitrogen]]</li>
<li>[[Liquid_nitrogen|Liquid nitrogen]]</li>
<li>[[Primary_antibodies|Primary antibodies]]</li>
<li>[[Primary_antibodies|Primary antibodies]]</li>
<li>[[Secondary_antibodies|Secondary antibodies]]</li>
<li>[[Secondary_antibodies|Secondary antibodies]]</li>
<li>[[Serum_immunostaining|Serum immunostaining]]</li>
<li>[[Serum_heat_inactivation|Serum heat inactivation]]</li>


=== Hardware ===
=== Hardware ===
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<li>[[Vacuum_pumps|Vacuum pumps]]</li>
<li>[[Vacuum_pumps|Vacuum pumps]]</li>
<li>[[Waterbath|Waterbath]]</li>
<li>[[Waterbath|Waterbath]]</li>
<li>[[RAMP Test|RAMP Test]]</li>


=== General ===
=== General ===
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</ul>
</ul>


== Antibodies ==
=== List of primary antibodies ===
{| class="wikitable sortable"
! Name !! Supplier !! Cat. No !! Host  !! Mono/Poly !! Antigen !! class="unsortable" | Contact person !! class="unsortable" | Storage temp !! class="unsortable" | Stock concentration !! class="unsortable" | Conditions for axolotl !! class="unsortable" | Conditions for Xenopus !! class="unsortable" | Conditions for mouse !! class="unsortable" | Conditions for cell culture !! class="unsortable" | Reference
|-
| 12/101 || Developmental Studies Hybridoma Bank ||  || Mouse ||  ||  || Yuka || 4°C || 46 ug/ml Ig || 1:200 || 1:200 ||  ||  ||  ||
|-
| 15.3B9 (NOT1) || Developmental Studies Hybridoma Bank || 15.3B9 (NOT1) || Mouse || Monoclonal || notochord marker (Chicken) || Yuka || 4°C ||  || 21 ug/ml IG ||  ||  ||  || http://dshb.biology.uiowa.edu/notochord-marker ||
|-
| 20B4 || Developmental Studies Hybridoma Bank || 20B4 || Mouse || Monoclonal || neural crest cell (Chicken) || Yuka || 4°C ||  ||  ||  ||  ||  || http://dshb.biology.uiowa.edu/neural-crest-cells ||
|-
| 5D3 || Developmental Studies Hybridoma Bank || 5D3 || Mouse || Monoclonal || Cadherin E (Xenopus) || Yuka || 4°C ||  || 37 ug/ml IG ||  ||  ||  || http://dshb.biology.uiowa.edu/5D3 ||
|-
| 8C8 || Developmental Studies Hybridoma Bank || 8C8 || Mouse || Monoclonal || integrin beta-1/ CD29 (Xenopus) || Yuka || 4°C ||  ||  ||  ||  ||  || http://dshb.biology.uiowa.edu/integrin-beta-1_7 ||
|-
| Aggrecan || millipore || AB1031 || Rabbit ||  ||  || Lidia ||  ||  ||  || Not work, Dim || '1:500 (Lidia) ||  ||  ||
|-
| Alpha tubulin (DM1a) || MPI ||  || Mouse || Monoclonal || Chicken alpha tubulin || Takuji || -20°C ||  ||  ||  ||  || 1:1000 -  ||  ||
|-
| b-catenin ||  Gift from Thomas Kurth || P14L || Rabbit ||  || Xenopus || Yuka_Aliquot from Tomas Kurth ||  ||  ||  ||  ||  ||  || Beta-catenin translocation into nuclei demarcates the dorsalizing centers in frog and fish embryos. ||
|-
| Bra ||  || AF2085 ||  ||  ||  || Yuka || -20C ||  || 0.2ug/ml in PBS ||  ||  ||  ||  ||
|-
| BrdU (Bu20a) || MPI ||  || Mouse || Monoclonal || BrdU - thymidine analog || Takuji || -20°C ||  || 1:400 -  ||  ||  ||  ||  ||
|-
| BrdU || Antibodies-online || ABIN964591 || Rabbit || Polyclonal || BrdU - thymidine analog || Takuji || -20°C ||  || 1:600 - ||  ||  ||  || http://www.antibodies-online.com/antibody/964591/anti-Bromodeoxyuridine+BrDU+antibody/ ||
|-
| Casp3 || Abcam || ab13847 || rabbit ||  ||  || Lidia || -20C ||  ||  ||  ||  ||  ||  ||
|-
| col1A2 || Developmental Studies Hybridoma Bank || SP1.D8 || Mouse || Monoclonal || Sheep || Yuka || -20C || 187ug/ml || 1:200- || 1:200_found in most connective tissue and abundant in bone, cornea, dermis and tendon. ||  ||  ||  ||
|-
| col2A1 || Acris || AM00619PU-N || Mouse ||  ||  || Yuka || -20C || 0.2mg/ml in /H2O || 1:10 || 1:100-200 ||  ||  ||  ||
|-
| Digoxigenin-AP || Roche || 11093274910 || Sheep || Polyclonal ||  || Common box || 4°C ||  ||  ||  ||  ||  || http://www.sigmaaldrich.com/catalog/product/roche/11093274910?lang=de&region=AT&gclid=Cj0KEQjwk-jGBRCbxoPLld_bp-IBEiQAgJaftdEIkv2iCvPxqx7NfQns9MUkipGFBChRXSL1FhsYOxkaApPb8P8HAQ ||
|-
| FITC || Jackson ImmunoResearch || 200-002-037 || Mouse || Monoclonal || Fluorescein isothiocyanate || Takuji || -20°C ||  || 1:400 -  ||  ||  ||  || https://www.jacksonimmuno.com/catalog/products/200-002-037 ||
|-
| FITC || invitrogen || 71-1900 || Rabbit || Polyclonal || Fluorescein isothiocyanate || Takuji || -20°C ||  || 1:400 -  ||  ||  ||  || https://www.thermofisher.com/antibody/product/FITC-Antibody-Polyclonal/71-1900 ||
|-
| GFP || Rockland || 600-401-215 || Rabbit ||  ||  || Common box || -20C ||  ||  || 1:2000-4000 ||  ||  ||  ||
|-
| GFP || MPI ||  || Goat ||  ||  || Yuka (from Jifeng) || -20C ||  || Yuka (from Jifeng) || 1:2000- ||  ||  ||  ||
|-
| GFP || MPI || 106-A20-Mix || Mouse ||  ||  || Yuka || -20C || 2.96 mg/ml in PBS ||  || 1:200, High background ||  ||  ||  ||
|-
| GFP || Abcam || ab13970 || Chick ||  ||  || Yuka (from Andrea), Lidia || -20C ||  || Andrea || High background ||  ||  ||  ||
|-
| GFP || Torrey Pines || TP401 || Rabbit ||  ||  || Yuka || -20C ||  || 1:200 (Axolotl) ||  ||  ||  ||  ||
|-
| GFP || Invitrogen || A11120 || Mouse || monoclonal ||  || Common box || -20C || 1 mg/ml in PBS ||  ||  ||  ||  ||  ||
|-
| Hoxa11 || Tanaka Lab (Kathleen) ||  || Rabbit || Polyclonal  || Axolotl || Yuka_Aliquot from Kathleen || -20C || 0.95 mg/ml ||  || FF+2%MEMFA.Dent's ||  ||  ||  ||
|-
| Hoxa11 || Tanaka Lab (Kathleen) ||  || Mouse || Monoclonal || Axolotl || Yuka_Aliquot from Kathleen || -20C || 4.22 mg/ml ||  ||  ||  ||  ||  ||
|-
| Hoxa13 || Tanaka Lab (Kathleen) ||  || Rabbit || Polyclonal  || Axolotl || Yuka_Aliquot from Kathleen || -20C || 0.15 mg/ml || 01:50 || 1:50, FreshFrozen+Unfixed ||  ||  ||  ||
|-
| Hoxa9 || Tanaka Lab (Kathleen) ||  || Rabbit || Polyclonal  || Axolotl || Yuka_Aliquot from Kathleen || -20C || 1.35 mg/ml ||  || FF+Methanol+ph9AR ||  ||  ||  ||
|-
| Laminin || Sigma || L9393 || Rabbit ||  ||  || Yuka (from Jifeng) || -20C ||  ||  || 1:200, 500_1:25 (paraffin), 1:100 (Slack) ||  ||  ||  ||
|-
| MBP || Genetex || GTX76114 || Rat || Monoclonal || Myelin basic protein (Bovine) || Common box || -20C ||  || 1:200 || 1:200 ||  ||  ||  ||
|-
| Mef2c || Sigma || HPA005533 || Rabbit || Polyclonal  || Human MEF2C (Myocyte enhancer factor 2C) || Aliquot from Takuji ||  ||  || 1:50 (Prayag), 1:300 (Takuji) || 1:5000,10000 (High background on all type of tissue) ||  ||  ||  ||
|-
| Meis 1/2/3 || Millipore || 05-779 || Mouse IgG1 || Monoclonal || mouse Meis 1 (aa 60-390) || Lidia || -20C (30% glycerol) ||  || 1:200 (Takuji?- frozen tissue secitons) ||  || 1:200 (Lidia?) ||  || http://www.merckmillipore.com/AT/de/product/Anti-Meis-1%2F2%2F3-Antibody%2C-clone-9.2.7,MM_NF-05-779?ReferrerURL=https%3A%2F%2Fwww.google.at%2F&bd=1 ||
|-
| MHC || Developmental Studies Hybridoma Bank || A4.1025 || Mouse ||  ||  || Yuka || 4°C ||  || 1:200 || 1:200 ||  ||  ||  ||
|-
| Osterix || abcam || ab22552 || rabbbit ||  ||  || Lidia ||  ||  ||  ||  ||  ||  ||  ||
|-
| Pax7 || MPI ||  || Mouse ||  ||  || Yuka || -20C ||  || 1:100, 200, 400  ||  ||  ||  ||  ||
|-
| PCNA || Santa Cruz || sc-56 AF64 || Alexa Fluor -647  ||  ||  || Lidia ||  ||  ||  || 1:500 ||  ||  ||  ||
|-
| PDGFRa (16A1) - Biotin || Invitrogen || A15732 || Mouse || Monoclonal || Human CD104a || Yuka (from Josh) || 4°C || 1 mg/ml ||  ||  ||  ||  || https://www.thermofisher.com/antibody/product/PDGFRA-Antibody-clone-16A1-Monoclonal/A15732 ||
|-
| Perilipin || R and D || P1873 || rabbit ||  ||  || Lidia ||  ||  ||  ||  ||  ||  ||  ||
|-
| PHH3 || millipore || 06-570 || rabbit || Polyclonal || Linear peptide corresponding to human Histone H3 at Ser10 || Takuji || 4°C || 1 mg/ml || 1:400 -  ||  ||  ||  || https://www.merckmillipore.com/DE/de/product/Anti-phospho-Histone-H3-%28Ser10%29-Antibody%2C-Mitosis-Marker,MM_NF-06-570?ReferrerURL=https%3A%2F%2Fwww.emdmillipore.com%2FCA%2Fen%2Fproduct%2FAnti-phospho-Histone-H3-%2528Ser10%2529-Antibody%252C-Mitosis-Marker%2CMM_NF-06-570 ||
|-
| PPARgamma || Cell signalling || 81B8 || rabbit ||  ||  || Lidia ||  ||  ||  ||  ||  ||  ||  ||
|-
| Prrx1 || Tanaka Lab (Prayag) ||  || Rabbit || Polyclonal || Axolotl N-terminus (1-101 aa) || Lidia, Yuka_Aliquot from Prayag || -20C ||  || 1:200 || 1:200 ||  ||  ||  ||
|-
| RFP || Rockland || 600-401-379 || Rabbit || Polyclonal ||  || Common box || -20C ||  || 1:300-1:1000 for Axolotl || 1:1000 or 1:2000 ||  ||  || http://www.rockland-inc.com/Product.aspx?id=34801 ||
|-
| Rhodamine || Molecular Probes || A-6397 || Rabbit || Polyclonal || Tetramethylrhodamine || Takuji || -20°C ||  || 1:400 -  ||  ||  ||  ||  ||
|-
| Scleraxis || Santa Cruz || D-14, sc-87425 || Goat || Polyclonal Goat IgG ||  || Yuka || 4°C ||  ||  ||  ||  ||  ||  ||
|-
| Shh (H-160) || Santa Cruz || SC-9024 || Rabbit || Polyclonal ||  || Yuka || 4°C ||  || 200 ug/ml ||  ||  ||  ||  ||
|-
| Sox9 || Chemicon || Ab5535 || Rabbit || Polyclonal || Synthetic peptide from human Sox9, aa486-509 (extreme C-Terminus) || Yuka_Aliquot || -20C ||  || 1:500-1:1000 || 1:500 ||  ||  || http://www.merckmillipore.com/DE/en/product/Anti-Sox9-Antibody,MM_NF-AB5535 ||
|-
| Sox9 || R&D || AF3075 || Goat || Polyclonal || E. coli-derived recombinant human SOX9 (Met1-Lys151) || Lidia, Yuka || -20C ||  || 1:100-1:200 || 1:100 ||  ||  || https://www.rndsystems.com/products/human-sox9-antibody_af3075 ||
|-
| Zo-1 || Invitrogen || 33-9100 || Mouse ||  ||  || Yuka (from Akira) || -20C ||  ||  ||  ||  ||  ||  ||
|-
| GADD45B || SIGMA || SAB2108614-100 || Rabbit || Polyclonal || QIHFT LIQSF CCDND INIVR VSGMQ RLAQL LGEPA ETQGT TEARD LHCLL || Marco || -20C || 0.5-1 mg/ml ||  ||  ||  ||  ||  ||
|-
| GADD45G || SIGMA || HPA023606 || Rabbit || Polyclonal || MTLEE VRGQD TVPES TARMQ GAGKA LHELL LSAQR QGCLT AGVYE SAKVL NVDPD NVTFC VLAAG EEDEG DIALQ IHFTL IQAFC CENDI DIVRV GDVQR LAAIV G || Marco || -20C || 0.05mg/ml ||  ||  ||  ||  ||  ||
|-
| TDG || SIGMA || HPA052263 || Rabbit || Polyclonal || WKCLF MSGLS EVQLN HMDDH TLPGK YGIGF TNMVE RTTPG SKDLS SKEFR EGGRI LVQKL QKYQP RIAVF NGKCI YEIFS KEVFG VKVKN LEFG || || -20C || 0.1mg/ml ||  ||  ||  ||  ||  ||
|-
| Tet3 || Diagenode || C15410311 || Rabbit || Polyclonal ||  || Marco || -20C || 1 ug/uL ||  ||  ||  ||  ||  ||
|-
| Tet2 || Diagenode || C15410255 || Rabbit || Polyclonal ||  || Marco || -20C || 1 ug/uL ||  ||  ||  ||  ||  ||
|-
| 5-mC || Diagenode || C15200081-100 || Mouse || Monoclonal ||  || Marco || -20C || 1.36 ug/ uL ||  ||  ||  ||  ||  ||
|-
| 5-hmC || Diagenode || C15410205-20 || Rabbit || Polyclonal ||  || Marco || -20C || 3.5 ug/uL ||  ||  ||  ||  ||  ||
|-
| IgG (Rabbit) || Diagenode || C15410206 || Rabbit || Polyclonal ||  || Marco || -20C || 1 ug/uL ||  ||  ||  ||  ||  ||
|-
| IgG (Rabbit) || CST || 2729S || Rabbit || Polyclonal ||  || Akane || -20C || 1-5ug/uL ||  ||  ||  ||  || https://media.cellsignal.com/pdf/2729.pdf#_ga=2.22008443.1736501072.1510317731-1668154722.1509367929 ||
|-
|anti-H3 (Rabbit) || Abcam || ab1791 || Rabbit || Polyclonal ||  || Akane || -20C || 1 ug/uL || 1:5000(WB), 1:1000 (CHiP), 1:1000 (Tissue IF)||  ||  ||  || Synthetic peptide corresponding to Human Histone H3 aa 100 to the C-terminus conjugated to Keyhole Limpet Haemocyanin (KLH).http://www.abcam.co.jp/histone-h3-antibody-nuclear-loading-control-and-chip-grade-ab1791.html ||
|-
|anti-H3K4me3 (Rabbit) || Abcam || ab8580 || Rabbit || Polyclonal ||  || Akane || -20C || 1 ug/uL || 1:1000 (WB), 1:250 (CHiP), 1:500 (Tissue IF)||  ||  ||  || Synthetic peptide within Human Histone H3 aa 1-100 (tri methyl K4) conjugated to Keyhole Limpet Haemocyanin (KLH). The exact sequence is proprietary.(http://www.abcam.co.jp/histone-h3-tri-methyl-k4-antibody-chip-grade-ab8580.html)||
|-
|anti-anti-H3K4me1 (Rabbit) ||　Abcam || ab8895||　Rabbit || Polyclonal ||  || Akane || -20C || 0,2 ug/uL || 1:500 (WB), 1:250 (CHiP), 1:500 (Tissue IF)||  ||  ||  || Synthetic peptide within Human Histone H3 aa 1-100 (mono methyl K4) conjugated to Keyhole Limpet Haemocyanin (KLH). http://www.abcam.co.jp/histone-h3-mono-methyl-k4-antibody-chip-grade-ab8895.html||
|-
|anti-H3K9me3 (Rabbit) || Abcam || ab8898|| Rabbit || Polyclonal ||  || Akane || -20C || 1 ug/uL || 1:1000 (WB), 1:500 (Tissue IF)||  ||  ||  || Synthetic peptide within Human Histone H3 aa 1-100 (N terminal) (tri methyl K9) conjugated to Keyhole Limpet Haemocyanin (KLH). The exact sequence is proprietary.
(Peptide available as ab1773) http://www.abcam.co.jp/histone-h3-tri-methyl-k9-antibody-chip-grade-ab8898.html||
|-
|anti-H3K27ac (Rabbit) || Abcam || ab4729|| Rabbit || Polyclonal ||  || Akane || -20C || 1 ug/uL || 1:1000 (WB), 1:500 (Tissue IF)||  ||  ||  || Synthetic peptide corresponding to Human Histone H3 aa 1-100 (acetyl K27) conjugated to Keyhole Limpet Haemocyanin (KLH). http://www.abcam.co.jp/histone-h3-acetyl-k27-antibody-chip-grade-ab4729.html||
|-
|anti-H3K27me3 (Rabbit) || millipore || 07-449 || Rabbit || Polyclonal ||  || Akane || -20C || 1 ug/uL || 1:1000 (WB), 1:500 (Tissue IF)||  ||  ||  || KLH-conjugated, synthetic 2X-branched peptide containing the sequence …AR(me3K)SAP… in which me3K corresponds to trimethyl-lysine at residue 27 of human histone H3. http://www.merckmillipore.com/AT/de/product/Anti-trimethyl-Histone-H3-Lys27-Antibody,MM_NF-07-449?ReferrerURL=https%3A%2F%2Fwww.google.at%2F&bd=1||
|-
|anti-Ezh2 mAB (mouse) || CST || CST3147  || mouse || mono clonal ||  || Akane || -20C || 1 ug/uL || WB, IF, ChIP DIDNT WORK ||  ||  ||  || https://www.cellsignal.com/products/primary-antibodies/ezh2-ac22-mouse-mab/3147 ||
|-
|Pol II antibody  (mouse) || CST || C15100055-100  || mouse|| mono clonal ||  || Akane || -20C || 1 ug/uL ||  ||  ||  ||  || mouse against the B1 subunit of RNA polymerase II (polymerase (RNA) II (DNA directed) polypeptide A) of wheat germ. Interacts with the highly conserved C-terminal domain of the protein containing the YSPTSPS repeat. https://www.diagenode.com/files/products/antibodies/Datasheet_PoII_C15100055.pdf||
|-
| IgG (mouse) || CST ||  || Rabit || Mono clonal || || Akane || -20C || 1 ug/uL || WB, IF, ChIP DIDNT WORK ||  ||  ||  ||  ||
|-
| CTCF (D31H2) XP®  || CST ||  CST-3418S|| Rabbit || Mono clonal ||  || Akane || -20C || 1 ug/uL || WB, IF, ChIP DIDNT WORK ||  ||  ||  ||  ||
|}


== Protocols ==
== Protocols ==
<ul>
<ul>
=== Cell culture ===
=== Cell culture ===
<li>[[Blastema_cells|Blastema cells]]</li>
<li>[[Adhesive_cell_culture|Adhesive cell culture]]</li>
<li>[[Baculovirus_titration|Baculovirus titration]]</li>
<li>[[Baculovirus_titration|Baculovirus titration]]</li>
<li>[[Cardiomyocyte_Preparation|Cardiomyocyte preparation]]</li>
<li>[[Electroporation_of_nec|Electroporation of neural epithelia cells (axolotl spinal cord)]]</li>
<li>[[Myoblasts_electroporation|Myoblasts electroporation]]</li>
<li>[[Myoblasts_electroporation|Myoblasts electroporation]]</li>
<li>[[Adhesive_cell_culture|Adhesive cell culture]]</li>
<li>[[Neurosphere_culture|Neurosphere culture]]</li>
<li>[[Thawing_293FT_cells|Thawing 293FT cells]]</li>
<li>[[G418_medium_preparation|G418 medium preparation]]</li>
<li>[[Fibronectin_Preparation|Fibronectin preparation]]</li>
<li>[[Gelatin Preparation|Gelatin preparation]]</li>
<li>[[Insulin_Preparation|Insulin preparation]]</li>
<li>[[Insulin_Preparation|Insulin preparation]]</li>
<li>[[Gelatin Embedding|Gelatin Embedding]]</li>
 
===== A1 cells =====
 
<li>[[Thawing_frozen_A1_cells|Thawing frozen A1 cells]]</li>
<li>[[Freezing_of_A1_cells|Freezing of A1 cells]]</li>
<li>[[Passaging_A1_cell|A1 cell passaging]]</li>
<li>[[A1_cell_passaging_myotube|A1 cell passaging for myotube preparation]]</li>
<li>[[Modified_myotube_prep|Modified myotube prep]]</li>
<li>[[A1_cell_transfection_with_FuGene|A1 cell transfection with FuGene]]</li>
<li>[[Electroporation_of_A1_cells|Electroporation of A1 cells]]</li>
<li>[[BrdU_labelling_of_A1_cells_in_96-well_plate|BrdU labelling of A1 cells in 96-well plate]]</li>
<li>[[BrdU_and_myosin_staining|BrdU and myosin staining]]</li>
<li>[[Preparation_of_Low_Serum_for_A1_cells|Preparation of Low Serum for A1 cells]]</li>
<li>[[Preparation_of_High_Serum_for_A1_cells|Preparation of High Serum for A1 cells]]</li>
<li>[[Preparation_of_Freezing_media_for_A1_cells|Preparation of Freezing media for A1 cells]]</li>
 
===== Blastema cells =====
<li>[[Blastema_cells|Blastema cells]]</li>
<li>[[Electroporation_of_blastema_cells|Electroporation of blastema cells]]</li>
<li>[[Electroporation_of_blastema_cells|Electroporation of blastema cells]]</li>
<li>[[Electroporation_of_nec|Electroporation of neural epithelia cells (axolotl spinal cord)]]</li>
 
===== C2C12 cells =====
 
<li>[[Thawing_frozen_C2C12_cells|Thawing frozen C2C12 cells]]</li>
<li>[[Freezing_of_C2C12_cells|Freezing of C2C12 cells]]</li>
<li>[[Passaging_C2C12_cells|C2C12 cell passaging]]</li>
<li>[[Myotube_preparation_of_C2C12_cells|Myotube preparation of C2C12 cells]]</li>
<li>[[C2C12_cell_transfection_with_FuGene|C2C12 cell transfection with FuGene]]</li>
<li>[[Cloning_of_C2C12_cells|Cloning of C2C12 cells]]</li>
<li>[[Electroporation_of_C2C12_cells|Electroporation of C2C12 cells]]</li>
<li>[[Preparation_of_Low_Serum_for_C2C12_cells|Preparation of Low Serum for C2C12 cells]]</li>
<li>[[Preparation_of_High_Serum_for_C2C12_cells|Preparation of High Serum for C2C12 cells]]</li>
<li>[[Preparation_of_Freezing_media_for_C2C12_cells|Preparation of Freezing media for C2C12 cells]]</li>
 
===== Embryonic stem cells =====
<li>[[mESC_culture|mESC culture/Cyst formation]]</li>
<li>[[mESC_culture|mESC culture/Cyst formation]]</li>
<li>[[Neurosphere_culture|Neurosphere culture]]</li>
 
===== Hybridoma cells =====
<li>[[Thawing_(XB10)_hybridoma_cells|Thawing (XB10) hybridoma cells]]</li>
<li>[[Hybridoma_cells_in_SFX_media|Hybridoma cells in SFX media]]</li>
<li>[[Hybridoma_cells_clones|Hybridoma cell clones]]</li>
 
=== Histology ===
=== Histology ===
<li>[[Alcian_Blue_Staining|Alcian Blue Staining]]</li>
<li>[[Double_Immunostaining_via_antigen_retrieval|Double Immunostaining via antigen retrieval (Sherry)]]</li>
<li>[[TSA_Staining_on_axolotl-tissue|Tyramide signal amplification (TSA) staining on axolotl tissue]]</li>
===== In situ Hybridization =====
<li>[[ISH_on_axolotl_tissue_sections|ISH on axolotl tissue sections (Anja)]]</li>
<li>[[ISH_on_axolotl_tissue_sections|ISH on axolotl tissue sections (Akira)]]</li>
<li>[[Whole_mount_ISH_on_axolotl_tissue|Whole mount ISH on axolotl tissue]]</li>
=== Antibodies ===
===== Monoclonal Antibodies =====
<li>[[Purifying IgG1 from Hybridoma Supernatant]]</li>
<li>[[Labelling myosin antibody]]</li>
<li>[[Labelling Pax6 with Dig-NHS]]</li>
<li>[[Anti-BrDU Antibody labeling]]</li>
===== Polyclonal Antibodies =====
<li>[[Address for making polyclonal antibodies]]</li>
<li>[[Letter to Froppier (French)]]</li>
<li>[[labeled AB staining]]</li>
<li>[[Antibody staining]]</li>
<li>[[Antibody purification]]</li>
<li>[[Antibody purification Sox2]]</li>
===== ELISA =====
<li>[[ELISA]]</li>
=== Molecular biology ===
=== Molecular biology ===
</ul>
<li>[[Metamorphosis_protocol|Metamorphosis protocol]]</li>
<li>[[Digestion_DNA|Plasmid digestion]]</li>
<li>[[RNA_Extraction_from_axolotl_tissue|RNA Extraction (axolotl tissue)]]</li>
<li>[[RNA_formaldehyde_gels|RNA formaldehyde gels]]</li>
<li>[[Amputation_andRNA_Isolation|Amputation and RNA Isolation]]</li>
<li>[[Linker Insertion|Linker Insertion]]</li>
<li>[[gRNA Production|gRNA Production]]</li>
<li>[[Cocktail Protocol for Pax7|Cocktail Protocol for Pax7]]</li>


 
== Genetics ==
== Booking calendars ==
=== Transgenic lines ===
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.
<ul>
<ul>
<li>
  <li>[[Transgenic_axolotl_lines|Axolotl (A.mexicanum)]]</li>
    Fluorescence microscopes
  <li>[[Transgenic_frog_lines|Frog (X.laevis)]]</li>
    <ul>
      <li>[http://www.my.calendars.net/olympusszx16 Olympus SZX 16]</li>
      <li>[http://www.my.calendars.net/new_olympus/ New Olympus SZX 16]</li>
      <li>[http://www.my.calendars.net/Olympus_OVK Olympus OVK]</li>
      <li>[http://www.my.calendars.net/axio_observer/ Axio Observer]</li>
    </ul>
</li>
<li>
    Microinjectors and electroporators
    <ul>
      <li>[http://www.my.calendars.net/electroporator Electroporator]</li>
      <li>[http://www.my.calendars.net/electroporator2 2nd electroporator]</li>
      <li>[http://www.my.calendars.net/microinjector Microinjector]</li>
      <li>[http://www.my.calendars.net/stereoscope2/d01/11/2012 Stereoscope]</li>
    </ul>
</li>
<li>
    Confocal microscopes
    <ul>
      <li>[http://www.my.calendars.net/leica_lsm Leica LSM]</li>
    </ul>
</li>
<li>
    Cryostats
    <ul>
      <li>[http://www.my.calendars.net/cryostat1 Cryostat 1]</li>
      <li>[http://www.my.calendars.net/cryostat2 Cryostat 2]</li>
    </ul>
</li>
<li>
  Microtome
  <ul>
      <li>[http://www.my.calendars.net/microtome Microtome]</li>
  </ul>
</li>
</ul>
</ul>


== Transgenic lines ==
=== Markers ===
=== Axolotl (A.mexicanum) ===
{| class="wikitable sortable"
{| class="wikitable sortable"
!style="width: 200px" | Name
!style="width: 150px" | Marker
!style="width: 300px" | Construct
!style="width: 250px" | Full name
!style="width: 200px" | Method of transgenesis
!style="width: 250px" | Target
!style="width: 150px" | Author
!style="width: 450px" | Remarks
!style="width: 200px" | Tissue
!style="width: 200px" | Link
!style="width: 300px" | Image
|-
!style="width: 300px" | Remarks
|DAPI/Hoechst
|4',6-diamidino-2-phenylindole
|Nuclei
|Incorporates into the DNA
|[http://en.wikipedia.org/wiki/DAPI DAPI], [http://en.wikipedia.org/wiki/Hoechst_stain Hoechst]
|-
|PCNA
|Proliferating-Cell-Nuclear-Antigen
|Dividing cells
|
|[http://en.wikipedia.org/wiki/PCNA PCNA]
|-
|SOX2
|SRY (sex determining region Y)-box 2
|Preferentially neuronal lineage
|Progenitor marker for both spinal cord and brain
|[http://en.wikipedia.org/wiki/Sox2 SOX2]
|-
|PAX6
|Paired box protein Pax-6
|Brain/spinal cord
|aka aniridia type II protein (AN2) or oculorhombin
|[http://en.wikipedia.org/wiki/Pax6 PAX6]
|-
|PAX7
|Paired box protein Pax-7
|Satellite cells/spinal cord/brain
|
|[http://en.wikipedia.org/wiki/PAX7 PAX7]
|-
|MHC
|Myosin heavy chain
|Muscle fibers
|
|[http://en.wikipedia.org/wiki/Myosin_heavy_chain MHC]
|-
|-
|PM28
|MYF5
|Prrx1-TFP-NLS-T2A-mERt-Cre-ERt
|Myogenic factor 5
|Sce1
|Myoblasts
|Prayag Murawala
|Regulates muscle differentiation, labels cycling myoblasts
|Limb bud and limb blastema
|[http://en.wikipedia.org/wiki/Myf5 MYF5]
|[[File:PM-28.png|180px|thumb|left|Limb bud expression]]
|Germ-line transmitted
|-
|-
|PM33
|TUBB3
|Col1A2-TFP-NLS-T2A-mERt-Cre-ERt
|ßIII-tubulin
|Sce1
|Axons
|Prayag Murawala
|
|Bone and fibroblast
|[http://en.wikipedia.org/wiki/TUBB3 TUBB3]
|[[File:PM-33 whole animal.png|80px|thumb|left|Bone expression]] [[File:PM-33.png|80px|thumb|left|Bone expression in Limb bud]]
|Germ-line transmitted
|-
|-
|MBP
|Myelin basic protein
|Schwann cells
|
|-
|PRRX1
|Paired mesoderm homeobox protein 1
|Connective tissue progenitors in Limb bud and Limb Blastema
|
|[http://en.wikipedia.org/wiki/PRRX1 PRRX1]
|-
|SMA
|Smooth muscle actin
|Blood vessels/endothelial cells
|
|
|-
|GFAP
|Glial fibrillary acidic protein
|Glia
|
|[http://en.wikipedia.org/wiki/Glial_fibrillary_acidic_protein GFAP]
|-
|NeuN
|Feminizing Locus on X-3, Fox-3, or Hexaribonucleotide Binding Protein-3
|Differentiated nerve
|
|[http://en.wikipedia.org/wiki/NeuN NeuN]
|-
|LEU7/HNK1/B3GAT1/CD57
|Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 1
|Schwann cells
|
|[http://en.wikipedia.org/wiki/B3GAT1 B3GAT1]
|-
|XBRA
|Xbrachyury
|Mesoderm during gastrula stage
|
|[http://en.wikipedia.org/wiki/Brachyury Brachyury]
|-
|MSX1
|Muscle segment homeobox, Msh homeobox 1
|Undifferentiated cells
|Transcriptional repressor during embryogenesis
|[http://en.wikipedia.org/wiki/MSX1 MSX1]
|-
|Trypan blue
|
|Dead tissues or cells
|Vital stain
|[http://en.wikipedia.org/wiki/Trypan_blue Trypan blue]
|-
|MEF2C
|Myocyte-specific enhancer factor 2C
|Differentiated muscle cells
|aka MADS box transcription enhancer factor 2, polypeptide C
|[http://en.wikipedia.org/wiki/Mef2c MEF2C]
|-
|PH3
|Phospho-Histone H3
|Mitotic cells
|
|
|-
|BrdU
|Bromodeoxyuridine
|Cells in S-phase
|
|[http://en.wikipedia.org/wiki/Brdu BrdU]
|-
|CASP3
|Caspase 3
|Dying cells
|
|[http://en.wikipedia.org/wiki/CASP3 CASP3]
|-
|GDF5
|Growth/differentiation factor 5
|Joints
|Joint development marker
|[http://en.wikipedia.org/wiki/GDF5 GDF5]
|-
|Survivin
|
|Cleavage furrow
|aka baculoviral inhibitor of apoptosis repeat-containing 5 or BIRC5
|[http://en.wikipedia.org/wiki/Survivin Survivin]
|-
|MAP2
|Microtubule-associated protein 2
|Neurons
|
|[http://en.wikipedia.org/wiki/MAP2 MAP2]
|-
|SOX9
|SRY (sex determining region Y)-box 2
|Cartillage progenitors
|
|[http://en.wikipedia.org/wiki/Sox9 SOX9]
|-
|MBP
|Myelin basic protein
|Myelin sheath
|
|[http://en.wikipedia.org/wiki/Myelin_basic_protein MBP]
|}
|}
=== Frog (X.levies) ===


== Digital data ==
== Digital data ==
Line 147: Line 438:
Select a category from the list below in order to view or download the data.
Select a category from the list below in order to view or download the data.


=== Presentations ===
=== Literature ===
{| class="wikitable sortable"
<ul>
!style="width: 200px" | Title
  <li>[[Literature#Theses|Theses]]</li>
!style="width: 400px" | Summary
  <li>[[Literature#Publications|Publications]]</li>
!style="width: 100px" | Author
</ul>
!style="width: 100px" | Date
!style="width: 100px" | Type
!style="width: 200px" | Link
|-
|Assembling the transcriptome: first results
|The presentation contains an overview of several commonly used sequencing and assembly methods. It also presents preliminary results.
|Sergej Novojilov
|Sep-04-2012
|Group meeting presentation
|tba
|-
|Assembling the transcriptome: first results
|The presentation contains an overview of several commonly used sequencing and assembly methods. It also presents preliminary results.
|Sergej Novojilov
|Sep-04-2012
|Group meeting presentation
|tba
|}
 
=== Theses ===
{| class="wikitable sortable"
!style="width: 200px" | Title
!style="width: 400px" | Summary
!style="width: 100px" | Author
!style="width: 200px" | Link
|-
|Test
|Test
|John Doe
|tba
|}


=== Databases ===
=== Databases ===
<ul>
<ul>
    <li>[https://axolotl-omics.org Axolotl transcriptome] website contains the Axolotl transcriptome assemblies</li>
    <li>[https://genome.axolotl-omics.org Axolotl genome] website contains the Axolotl genome assemblies</li>
    <li>[http://newtomics.mpi-bn.mpg.de/ Newt transcriptome] website contains the Newt transcriptome assembly</li>
    <li>[http://sandberg.cmb.ki.se/redspottednewt/ Red spotted newt transcriptome] website contains the red spotted newt transcriptome assembly</li>
     <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>
     <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>
     <li>[http://est.age.mpg.de/cgi-bin/result.py Axologle] database contains several different Axolotl transciptome assemblies</li>
     <li>[http://python-srv1.mpi-cbg.de/axolotl/cgi-bin/login.cgi?dispatch=contig_search.cgi Short insert cDNA library]</li>
    <li>[https://axologl.axolotl-omics.org Axologle] database contains expression profiling data of Axolotl limb regeneration</li>
    <li>[https://axologl.axolotl-omics.org/blast/blast.html Axolotl BLAST] database contains several different BLAST-able Axolotl transciptome assemblies</li>
</ul>
</ul>


=== Datasets ===
=== Datasets ===
==== Next generation sequencing ====
<ul>
<ul>
    <li>Mature and regenerating spinal cord
  <li>[[Datasets#Sequences|Sequences]]
      <ul>
        <li>[[Datasets#Illumina|Illumina]]</li>
        <li>[[Datasets#Sanger|Sanger]]</li>
        <li>[[Datasets#Roche.2F454|Roche/454]]</li>
      </ul>
  </li>
  <li>[[Datasets#Microarrays|Microarrays]]
</ul>


        {| class="wikitable"
=== Interesting links ===
        !style="width: 200px" | Name
<ul>
        !style="width: 400px" | Description
  <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>
        !style="width: 100px" | Type
        !style="width: 100px" | Reads
        !style="width: 200px" | Links
        !style="width: 100px" | Author
        !style="width: 300px" | Remarks
        |-
        |Mature spinal cord
        |Mature axolotl spinal cord
        |Illumina, paired-end, 100bp
        |65,753,941
        |tba
        |Akira Tazaki
        |
        |- 
        |Injured spinal cord
        |Injured axolotl spinal cord, 6dpi
        |Illumina, paired-end, 100bp
        |78,459,950
        |tba
        |Akira Tazaki
        |}
    </li>
    <li>Axolotl limb
 
        {| class="wikitable"
        !style="width: 200px" | Name
        !style="width: 400px" | Description
        !style="width: 100px" | Type
        !style="width: 100px" | Reads
        !style="width: 200px" | Links
        !style="width: 100px" | Author
        !style="width: 300px" | Remarks
        |-
        |Mature limb
        |Mature axolotl forelimb
        |Illumina, single-end, 76bp
        |65,934,228
        |tba
        |Dunja Knapp
        |
        |-
        |Amputated limb (36h)
        |Amputated axolotl forelimb (36hpa)
        |Illumina, single-end, 76bp
        |65,250,768
        |tba
        |Dunja Knapp
        |
        |-
        |Amputated limb (72h)
        |Amputated axolotl forelimb (72hpa)
        |Illumina, single-end, 76bp
        |62,970,898
        |tba
        |Dunja Knapp
        |
        |-
        |Lateral wound (36h)
        |Injured (lateral wound) axolotl forelimb (36hpw)
        |Illumina, single-end, 76bp
        |66,361,470
        |tba
        |Dunja Knapp
        |
        |-
        |Lateral wound (72h)
        |Injured (lateral wound) axolotl forelimb (72hpw)
        |Illumina, single-end, 76bp
        |64,133,834
        |tba
        |Dunja Knapp
        |
        |}
    </li>
</ul>
</ul>
=== Images ===
==== In-situ images ====
==== Antibody staining ====
== Change list ==
This section is an attempt to make people catalog the changes they might have introduced to the data, protocols, chemicals and so on.

Latest revision as of 15:37, 19 July 2022

Introduction

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.

Lab duties

Antibodies

List of primary antibodies

Name Supplier Cat. No Host Mono/Poly Antigen Contact person Storage temp Stock concentration Conditions for axolotl Conditions for Xenopus Conditions for mouse Conditions for cell culture Reference
12/101 Developmental Studies Hybridoma Bank Mouse Yuka 4°C 46 ug/ml Ig 1:200 1:200
15.3B9 (NOT1) Developmental Studies Hybridoma Bank 15.3B9 (NOT1) Mouse Monoclonal notochord marker (Chicken) Yuka 4°C 21 ug/ml IG http://dshb.biology.uiowa.edu/notochord-marker
20B4 Developmental Studies Hybridoma Bank 20B4 Mouse Monoclonal neural crest cell (Chicken) Yuka 4°C http://dshb.biology.uiowa.edu/neural-crest-cells
5D3 Developmental Studies Hybridoma Bank 5D3 Mouse Monoclonal Cadherin E (Xenopus) Yuka 4°C 37 ug/ml IG http://dshb.biology.uiowa.edu/5D3
8C8 Developmental Studies Hybridoma Bank 8C8 Mouse Monoclonal integrin beta-1/ CD29 (Xenopus) Yuka 4°C http://dshb.biology.uiowa.edu/integrin-beta-1_7
Aggrecan millipore AB1031 Rabbit Lidia Not work, Dim '1:500 (Lidia)
Alpha tubulin (DM1a) MPI Mouse Monoclonal Chicken alpha tubulin Takuji -20°C 1:1000 -
b-catenin Gift from Thomas Kurth P14L Rabbit Xenopus Yuka_Aliquot from Tomas Kurth Beta-catenin translocation into nuclei demarcates the dorsalizing centers in frog and fish embryos.
Bra AF2085 Yuka -20C 0.2ug/ml in PBS
BrdU (Bu20a) MPI Mouse Monoclonal BrdU - thymidine analog Takuji -20°C 1:400 -
BrdU Antibodies-online ABIN964591 Rabbit Polyclonal BrdU - thymidine analog Takuji -20°C 1:600 - http://www.antibodies-online.com/antibody/964591/anti-Bromodeoxyuridine+BrDU+antibody/
Casp3 Abcam ab13847 rabbit Lidia -20C
col1A2 Developmental Studies Hybridoma Bank SP1.D8 Mouse Monoclonal Sheep Yuka -20C 187ug/ml 1:200- 1:200_found in most connective tissue and abundant in bone, cornea, dermis and tendon.
col2A1 Acris AM00619PU-N Mouse Yuka -20C 0.2mg/ml in /H2O 1:10 1:100-200
Digoxigenin-AP Roche 11093274910 Sheep Polyclonal Common box 4°C http://www.sigmaaldrich.com/catalog/product/roche/11093274910?lang=de&region=AT&gclid=Cj0KEQjwk-jGBRCbxoPLld_bp-IBEiQAgJaftdEIkv2iCvPxqx7NfQns9MUkipGFBChRXSL1FhsYOxkaApPb8P8HAQ
FITC Jackson ImmunoResearch 200-002-037 Mouse Monoclonal Fluorescein isothiocyanate Takuji -20°C 1:400 - https://www.jacksonimmuno.com/catalog/products/200-002-037
FITC invitrogen 71-1900 Rabbit Polyclonal Fluorescein isothiocyanate Takuji -20°C 1:400 - https://www.thermofisher.com/antibody/product/FITC-Antibody-Polyclonal/71-1900
GFP Rockland 600-401-215 Rabbit Common box -20C 1:2000-4000
GFP MPI Goat Yuka (from Jifeng) -20C Yuka (from Jifeng) 1:2000-
GFP MPI 106-A20-Mix Mouse Yuka -20C 2.96 mg/ml in PBS 1:200, High background
GFP Abcam ab13970 Chick Yuka (from Andrea), Lidia -20C Andrea High background
GFP Torrey Pines TP401 Rabbit Yuka -20C 1:200 (Axolotl)
GFP Invitrogen A11120 Mouse monoclonal Common box -20C 1 mg/ml in PBS
Hoxa11 Tanaka Lab (Kathleen) Rabbit Polyclonal Axolotl Yuka_Aliquot from Kathleen -20C 0.95 mg/ml FF+2%MEMFA.Dent's
Hoxa11 Tanaka Lab (Kathleen) Mouse Monoclonal Axolotl Yuka_Aliquot from Kathleen -20C 4.22 mg/ml
Hoxa13 Tanaka Lab (Kathleen) Rabbit Polyclonal Axolotl Yuka_Aliquot from Kathleen -20C 0.15 mg/ml 01:50 1:50, FreshFrozen+Unfixed
Hoxa9 Tanaka Lab (Kathleen) Rabbit Polyclonal Axolotl Yuka_Aliquot from Kathleen -20C 1.35 mg/ml FF+Methanol+ph9AR
Laminin Sigma L9393 Rabbit Yuka (from Jifeng) -20C 1:200, 500_1:25 (paraffin), 1:100 (Slack)
MBP Genetex GTX76114 Rat Monoclonal Myelin basic protein (Bovine) Common box -20C 1:200 1:200
Mef2c Sigma HPA005533 Rabbit Polyclonal Human MEF2C (Myocyte enhancer factor 2C) Aliquot from Takuji 1:50 (Prayag), 1:300 (Takuji) 1:5000,10000 (High background on all type of tissue)
Meis 1/2/3 Millipore 05-779 Mouse IgG1 Monoclonal mouse Meis 1 (aa 60-390) Lidia -20C (30% glycerol) 1:200 (Takuji?- frozen tissue secitons) 1:200 (Lidia?) http://www.merckmillipore.com/AT/de/product/Anti-Meis-1%2F2%2F3-Antibody%2C-clone-9.2.7,MM_NF-05-779?ReferrerURL=https%3A%2F%2Fwww.google.at%2F&bd=1
MHC Developmental Studies Hybridoma Bank A4.1025 Mouse Yuka 4°C 1:200 1:200
Osterix abcam ab22552 rabbbit Lidia
Pax7 MPI Mouse Yuka -20C 1:100, 200, 400
PCNA Santa Cruz sc-56 AF64 Alexa Fluor -647 Lidia 1:500
PDGFRa (16A1) - Biotin Invitrogen A15732 Mouse Monoclonal Human CD104a Yuka (from Josh) 4°C 1 mg/ml https://www.thermofisher.com/antibody/product/PDGFRA-Antibody-clone-16A1-Monoclonal/A15732
Perilipin R and D P1873 rabbit Lidia
PHH3 millipore 06-570 rabbit Polyclonal Linear peptide corresponding to human Histone H3 at Ser10 Takuji 4°C 1 mg/ml 1:400 - https://www.merckmillipore.com/DE/de/product/Anti-phospho-Histone-H3-%28Ser10%29-Antibody%2C-Mitosis-Marker,MM_NF-06-570?ReferrerURL=https%3A%2F%2Fwww.emdmillipore.com%2FCA%2Fen%2Fproduct%2FAnti-phospho-Histone-H3-%2528Ser10%2529-Antibody%252C-Mitosis-Marker%2CMM_NF-06-570
PPARgamma Cell signalling 81B8 rabbit Lidia
Prrx1 Tanaka Lab (Prayag) Rabbit Polyclonal Axolotl N-terminus (1-101 aa) Lidia, Yuka_Aliquot from Prayag -20C 1:200 1:200
RFP Rockland 600-401-379 Rabbit Polyclonal Common box -20C 1:300-1:1000 for Axolotl 1:1000 or 1:2000 http://www.rockland-inc.com/Product.aspx?id=34801
Rhodamine Molecular Probes A-6397 Rabbit Polyclonal Tetramethylrhodamine Takuji -20°C 1:400 -
Scleraxis Santa Cruz D-14, sc-87425 Goat Polyclonal Goat IgG Yuka 4°C
Shh (H-160) Santa Cruz SC-9024 Rabbit Polyclonal Yuka 4°C 200 ug/ml
Sox9 Chemicon Ab5535 Rabbit Polyclonal Synthetic peptide from human Sox9, aa486-509 (extreme C-Terminus) Yuka_Aliquot -20C 1:500-1:1000 1:500 http://www.merckmillipore.com/DE/en/product/Anti-Sox9-Antibody,MM_NF-AB5535
Sox9 R&D AF3075 Goat Polyclonal E. coli-derived recombinant human SOX9 (Met1-Lys151) Lidia, Yuka -20C 1:100-1:200 1:100 https://www.rndsystems.com/products/human-sox9-antibody_af3075
Zo-1 Invitrogen 33-9100 Mouse Yuka (from Akira) -20C
GADD45B SIGMA SAB2108614-100 Rabbit Polyclonal QIHFT LIQSF CCDND INIVR VSGMQ RLAQL LGEPA ETQGT TEARD LHCLL Marco -20C 0.5-1 mg/ml
GADD45G SIGMA HPA023606 Rabbit Polyclonal MTLEE VRGQD TVPES TARMQ GAGKA LHELL LSAQR QGCLT AGVYE SAKVL NVDPD NVTFC VLAAG EEDEG DIALQ IHFTL IQAFC CENDI DIVRV GDVQR LAAIV G Marco -20C 0.05mg/ml
TDG SIGMA HPA052263 Rabbit Polyclonal WKCLF MSGLS EVQLN HMDDH TLPGK YGIGF TNMVE RTTPG SKDLS SKEFR EGGRI LVQKL QKYQP RIAVF NGKCI YEIFS KEVFG VKVKN LEFG -20C 0.1mg/ml
Tet3 Diagenode C15410311 Rabbit Polyclonal Marco -20C 1 ug/uL
Tet2 Diagenode C15410255 Rabbit Polyclonal Marco -20C 1 ug/uL
5-mC Diagenode C15200081-100 Mouse Monoclonal Marco -20C 1.36 ug/ uL
5-hmC Diagenode C15410205-20 Rabbit Polyclonal Marco -20C 3.5 ug/uL
IgG (Rabbit) Diagenode C15410206 Rabbit Polyclonal Marco -20C 1 ug/uL
IgG (Rabbit) CST 2729S Rabbit Polyclonal Akane -20C 1-5ug/uL https://media.cellsignal.com/pdf/2729.pdf#_ga=2.22008443.1736501072.1510317731-1668154722.1509367929
anti-H3 (Rabbit) Abcam ab1791 Rabbit Polyclonal Akane -20C 1 ug/uL 1:5000(WB), 1:1000 (CHiP), 1:1000 (Tissue IF) Synthetic peptide corresponding to Human Histone H3 aa 100 to the C-terminus conjugated to Keyhole Limpet Haemocyanin (KLH).http://www.abcam.co.jp/histone-h3-antibody-nuclear-loading-control-and-chip-grade-ab1791.html
anti-H3K4me3 (Rabbit) Abcam ab8580 Rabbit Polyclonal Akane -20C 1 ug/uL 1:1000 (WB), 1:250 (CHiP), 1:500 (Tissue IF) Synthetic peptide within Human Histone H3 aa 1-100 (tri methyl K4) conjugated to Keyhole Limpet Haemocyanin (KLH). The exact sequence is proprietary.(http://www.abcam.co.jp/histone-h3-tri-methyl-k4-antibody-chip-grade-ab8580.html)
anti-anti-H3K4me1 (Rabbit) 　Abcam ab8895 　Rabbit Polyclonal Akane -20C 0,2 ug/uL 1:500 (WB), 1:250 (CHiP), 1:500 (Tissue IF) Synthetic peptide within Human Histone H3 aa 1-100 (mono methyl K4) conjugated to Keyhole Limpet Haemocyanin (KLH). http://www.abcam.co.jp/histone-h3-mono-methyl-k4-antibody-chip-grade-ab8895.html
anti-H3K9me3 (Rabbit) Abcam ab8898 Rabbit Polyclonal Akane -20C 1 ug/uL 1:1000 (WB), 1:500 (Tissue IF) Synthetic peptide within Human Histone H3 aa 1-100 (N terminal) (tri methyl K9) conjugated to Keyhole Limpet Haemocyanin (KLH). The exact sequence is proprietary.

(Peptide available as ab1773) http://www.abcam.co.jp/histone-h3-tri-methyl-k9-antibody-chip-grade-ab8898.html%7C%7C

anti-H3K27ac (Rabbit) Abcam ab4729 Rabbit Polyclonal Akane -20C 1 ug/uL 1:1000 (WB), 1:500 (Tissue IF) Synthetic peptide corresponding to Human Histone H3 aa 1-100 (acetyl K27) conjugated to Keyhole Limpet Haemocyanin (KLH). http://www.abcam.co.jp/histone-h3-acetyl-k27-antibody-chip-grade-ab4729.html
anti-H3K27me3 (Rabbit) millipore 07-449 Rabbit Polyclonal Akane -20C 1 ug/uL 1:1000 (WB), 1:500 (Tissue IF) KLH-conjugated, synthetic 2X-branched peptide containing the sequence …AR(me3K)SAP… in which me3K corresponds to trimethyl-lysine at residue 27 of human histone H3. http://www.merckmillipore.com/AT/de/product/Anti-trimethyl-Histone-H3-Lys27-Antibody,MM_NF-07-449?ReferrerURL=https%3A%2F%2Fwww.google.at%2F&bd=1
anti-Ezh2 mAB (mouse) CST CST3147 mouse mono clonal Akane -20C 1 ug/uL WB, IF, ChIP DIDNT WORK https://www.cellsignal.com/products/primary-antibodies/ezh2-ac22-mouse-mab/3147
Pol II antibody (mouse) CST C15100055-100 mouse mono clonal Akane -20C 1 ug/uL mouse against the B1 subunit of RNA polymerase II (polymerase (RNA) II (DNA directed) polypeptide A) of wheat germ. Interacts with the highly conserved C-terminal domain of the protein containing the YSPTSPS repeat. https://www.diagenode.com/files/products/antibodies/Datasheet_PoII_C15100055.pdf
IgG (mouse) CST Rabit Mono clonal Akane -20C 1 ug/uL WB, IF, ChIP DIDNT WORK
CTCF (D31H2) XP® CST CST-3418S Rabbit Mono clonal Akane -20C 1 ug/uL WB, IF, ChIP DIDNT WORK

Protocols

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