Overview: Difference between revisions

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=== Datasets ===
=== Datasets ===
==== Sequences ====
<ul>
===== Illumina =====
  <li>[[Datasets#Sequences|Sequences]]
The data can be found under <b>//biodata/groups/crtd_tanaka/LabData/Sequencing/Illumina</b>.
      <ul>
        {| class="wikitable sortable"
        <li>[[Datasets#Illumina|Illumina]]</li>
        !style="width: 200px" class="unsortable" | Name
        <li>[[Datasets#Sanger|Sanger]]</li>
        !style="width: 300px" class="unsortable" | Description
         <li>[[Datasets#Roche.2F454|Roche/454]]</li>
        !style="width: 200px"                    | Tissue
      </ul>
        !style="width: 90px"  class="unsortable" | Type
  </li>
        !style="width: 80px"  class="unsortable" | Read length
  <li>[[Datasets#Microarrays|Microarrays]]
        !style="width: 100px"                    | Reads
</ul>
        !style="width: 100px" class="unsortable" | Format
        !style="width: 200px" class="unsortable" | Location
        !style="width: 100px"                    | Author
        !style="width: 300px" class="unsortable" | Remarks
        |-
        |Mature spinal cord
        |Mature axolotl spinal cord
        |Spinal cord
        |Paired-ended
        |100bp
        |65,753,941
        |FastQ
        |SpinalCord/mSC.fastq.tar.gz
        |Akira Tazaki
        |
        |- 
        |Injured spinal cord
        |Injured axolotl spinal cord, 6dpi
        |Spinal cord
        |Paired-ended
        |100bp
        |78,459,950
        |FastQ
        |SpinalCord/6diSC.fastq.tar.gz
        |Akira Tazaki
        |
        |-
        |Mature spinal cord
        |Mature axolotl spinal cord, replicate 2, crossing 142x5
        |Spinal cord
        |Paired-ended
        |100bp
        |101,769,559
        |FastQ
        |SpinalCord/mSC_142x5.fastq.tar.gz
        |Akira Tazaki
        |Due to a sequencer failure only the first 66 bases are safe
        |- 
        |Mature spinal cord
        |Mature axolotl spinal cord, replicate 3, crossing 96x6
        |Spinal cord
        |Paired-ended
        |100bp
        |95,946,545
        |FastQ
        |SpinalCord/mSC_96x6.fastq.tar.gz
        |Akira Tazaki
        |Due to a sequencer failure only the first 66 bases are safe
        |- 
        |Injured spinal cord
        |Injured axolotl spinal cord, 6dpi, replicate 2, crossing 142x5
        |Spinal cord
        |Paired-ended
        |100bp
        |96,626,387
        |FastQ
        |SpinalCord/6diSC_142x5.fastq.tar.gz
        |Akira Tazaki
        |Due to a sequencer failure only the first 66 bases are safe
        |- 
        |Injured spinal cord
        |Injured axolotl spinal cord, 6dpi, replicate 3, crossing 96x5
        |Spinal cord
        |Paired-ended
        |100bp
        |99,855,603
        |FastQ
        |SpinalCord/6diSC_96x5.fastq.tar.gz
        |Akira Tazaki
        |Due to a sequencer failure only the first 66 bases are safe
        |-
        |Mature limb
        |Mature axolotl forelimb
        |Limb
        |Single-ended
        |76bp
        |65,934,228
        |FastQ
        |Limb/Mature.fastq.tar.gz
        |Dunja Knapp
        |
        |-
        |Amputated limb (36h)
        |Amputated axolotl forelimb (36hpa)
        |Limb
        |Single-ended
        |76bp
        |65,250,768
        |FastQ
        |Limb/36h_amp.fastq.tar.gz
        |Dunja Knapp
        |
        |-
        |Amputated limb (72h)
        |Amputated axolotl forelimb (72hpa)
        |Limb
        |Single-ended
        |76bp
        |62,970,898
        |FastQ
        |Limb/72h_amp.fastq.tar.gz
        |Dunja Knapp
        |
        |-
        |Lateral wound (36h)
        |Injured (lateral wound) axolotl forelimb (36hpw)
        |Limb
        |Single-ended
        |76bp
        |66,361,470
        |FastQ
        |Limb/36h_lw.fastq.tar.gz
        |Dunja Knapp
        |
        |-
        |Lateral wound (72h)
        |Injured (lateral wound) axolotl forelimb (72hpw)
        |Limb
        |Single-ended
        |76bp
        |64,133,834
        |FastQ
        |Limb/72h_lw.fastq.tar.gz
        |Dunja Knapp
        |
        |}
 
===== Sanger =====
The data can be found under <b>//biodata/groups/crtd_tanaka/LabData/Sequencing/Sanger</b>.
        {| class="wikitable sortable"
        !style="width: 200px" class="unsortable" | Name
        !style="width: 300px" class="unsortable" | Description
        !style="width: 200px"                    | Tissue
        !style="width: 200px"                    | Sequences
        !style="width: 300px" class="unsortable" | Location
        !style="width: 100px"                    | Author
        !style="width: 300px" class="unsortable" | Remarks
        |-
        |LimbBlastema
        |Limb blastema library
        |Limb blastema
        |20160 (RSD) / 15648 (SCF)
        |<ul><li>SCF files: LimbBlastema/LB_SCF.gz</li><li>RSD files: LimbBlastema/LB_RSD.gz</li></ul>
        |Akira Tazaki
        |
        |-
        |NeuraTube
        |Neural tube library
        |Teural tube
        |4896 (RSD) / 7905 (SCF)
         |<ul><li>SCF files: NeuralTube/NT_SCF.gz</li><li>RSD files: NeuralTube/NT_RSD.gz</li></ul>
        |Akira Tazaki
        |
        |}
 
===== Roche/454 =====
The data can be found under <b>//biodata/groups/crtd_tanaka/LabData/Sequencing/454</b>.
        {| class="wikitable"
        !style="width: 200px" | Name
        !style="width: 300px" | Description
        !style="width: 200px" | Tissue
        !style="width: 200px" | Reads
        !style="width: 200px" | Format
        !style="width: 300px" | Location
        !style="width: 100px" | Author
        !style="width: 300px" | Remarks
        |-
        |454
        |Mixed 454
        |Mixed
        |1,208,954
        |Fasta/Qual
        |Ax_454.tar.gz
        |n/a
        |}
 
==== Microarrays ====
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.
        {| class="wikitable"
        !style="width: 200px" | Name
        !style="width: 300px" | Description
        !style="width: 300px" | Timepoints
        !style="width: 200px" | Tissue
        !style="width: 110px" | Array type
        !style="width: 250px" | Location
        !style="width: 100px" | Author
        !style="width: 300px" | Remarks
        |-
        |Fin vs bulk
        |Timecourse microarray experiment using fin and bulk tissue
        |0, 1d, 3d
        |Mature tail: fin and bulk
        |Agilent, 44000
        |Fin_vs_bulk
        |Eugeniu Nacu
        |
        |-
        |Limb
        |Timecourse microarray experiment using limb
        |0, 3h, 6h, 12h, 24h, 36h, 52h, 72h, 120h, 168h, 288h, 528h
        |Mature limb
        |Agilent, 44000
        |Limb_timecourse
        |Eugeniu Nacu
        |
        |-
        |Tail timecourse
        |Timecourse microarray experiment using tail
        |0, 3h, 6h, 12h, 18h, 24h, 36h, 48h, 72h, 120h, 168h, 288h
        |Mature tail
        |Agilent, 44000
        |Tail_timecourse
        |Eugeniu Nacu
        |
        |-
        |Limb timecourse 2
        |Timecourse microarray experiment using limb
        |0, 3h, 6h, 9h, 12h, 24h, 36h, 52h, 72h, 120h, 168h, 288h, 528h
        |Mature limb and limb bud
        |Agilent, 44000
        |Limb_timecourse_2
        |Dunja Knapp
        |
        |}

Revision as of 11:05, 29 January 2013

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.

Axolotl

Lab duties


Protocols


Booking calendars

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.

Transgenic lines

Digital data

Over the years the members of the lab have produced a lot of different data: Sanger sequences, EST libraries, images and so on. Select a category from the list below in order to view or download the data.

Literature

Databases

  • 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.
  • Axologle database contains several different Axolotl transciptome assemblies

Datasets

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