Datasets: Difference between revisions

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         !style="width: 90px"  class="unsortable" | Type
         !style="width: 90px"  class="unsortable" | Type
         !style="width: 80px"  class="unsortable" | Read length
         !style="width: 80px"  class="unsortable" | Read length
        !style="width: 100px"  class="unsortable"| Fragment size
         !style="width: 100px"                    | Reads
         !style="width: 100px"                    | Reads
         !style="width: 100px" class="unsortable" | Format
         !style="width: 100px" class="unsortable" | Format
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         |Paired-ended
         |Paired-ended
         |100bp
         |100bp
        |n/a
         |65,753,941
         |65,753,941
         |FastQ
         |FastQ
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         |Paired-ended
         |Paired-ended
         |100bp
         |100bp
        |n/a
         |78,459,950
         |78,459,950
         |FastQ
         |FastQ
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         |Paired-ended
         |Paired-ended
         |100bp
         |100bp
        |180bp
         |101,769,559
         |101,769,559
         |FastQ
         |FastQ
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         |Paired-ended
         |Paired-ended
         |100bp
         |100bp
        |180bp
         |95,946,545
         |95,946,545
         |FastQ
         |FastQ
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         |Paired-ended
         |Paired-ended
         |100bp
         |100bp
        |180bp
         |96,626,387
         |96,626,387
         |FastQ
         |FastQ
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         |Paired-ended
         |Paired-ended
         |100bp
         |100bp
        |180bp
         |99,855,603
         |99,855,603
         |FastQ
         |FastQ
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         |Single-ended
         |Single-ended
         |76bp
         |76bp
        |n/a
         |65,934,228
         |65,934,228
         |FastQ
         |FastQ
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         |Single-ended
         |Single-ended
         |76bp
         |76bp
        |n/a
         |65,250,768
         |65,250,768
         |FastQ
         |FastQ
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         |Single-ended
         |Single-ended
         |76bp
         |76bp
        |n/a
         |62,970,898
         |62,970,898
         |FastQ
         |FastQ
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         |Single-ended
         |Single-ended
         |76bp
         |76bp
        |n/a
         |66,361,470
         |66,361,470
         |FastQ
         |FastQ
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         |Single-ended
         |Single-ended
         |76bp
         |76bp
        |n/a
         |64,133,834
         |64,133,834
         |FastQ
         |FastQ
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         |Single-ended
         |Single-ended
         |
         |
        |180bp
         |
         |
         |FastQ
         |FastQ
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         |Single-ended
         |Single-ended
         |
         |
        |180bp
         |
         |
         |FastQ
         |FastQ
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         |Single-ended
         |Single-ended
         |
         |
        |180bp
         |
         |
         |FastQ
         |FastQ
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         |Single-ended
         |Single-ended
         |
         |
        |180bp
         |
         |
         |FastQ
         |FastQ
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         |Single-ended
         |Single-ended
         |
         |
        |180bp
         |
         |
         |FastQ
         |FastQ

Revision as of 15:22, 31 January 2013

Sequences

Illumina

The data can be found under //biodata/groups/crtd_tanaka/LabData/Sequencing/Illumina.

Name Description Tissue Type Read length Fragment size Reads Format Location Author Remarks
Mature spinal cord Mature axolotl spinal cord Spinal cord Paired-ended 100bp n/a 65,753,941 FastQ SpinalCord/mSC.fastq.tar.gz Akira Tazaki
Injured spinal cord Injured axolotl spinal cord, 6dpi Spinal cord Paired-ended 100bp n/a 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 180bp 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 180bp 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 180bp 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 180bp 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 n/a 65,934,228 FastQ Limb/Mature.fastq.tar.gz Dunja Knapp
Amputated limb (36h) Amputated axolotl forelimb (36hpa) Limb Single-ended 76bp n/a 65,250,768 FastQ Limb/36h_amp.fastq.tar.gz Dunja Knapp
Amputated limb (72h) Amputated axolotl forelimb (72hpa) Limb Single-ended 76bp n/a 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 n/a 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 n/a 64,133,834 FastQ Limb/72h_lw.fastq.tar.gz Dunja Knapp
LPM-transplant Blastema samples of a LPM-transplanted animal: mature and 1dpa Blastema Single-ended 180bp FastQ LPM/An3.fastq.tar.gz Prayag Murawala/Dunja Knapp GFP-labeled LPM was transplanted to a white-host embryo. The limb of the host was amputated and the blastema sample was collected.
LPM-transplant Blastema samples of a LPM-transplanted animal: mature and 10dpa Blastema Single-ended 180bp FastQ LPM/An4.fastq.tar.gz Prayag Murawala/Dunja Knapp GFP-labeled LPM was transplanted to a white-host embryo. The limb of the host was amputated and the blastema sample was collected.
LPM-transplant Blastema samples of a LPM-transplanted animal: mature and 5dpa Blastema Single-ended 180bp FastQ LPM/An6.fastq.tar.gz Prayag Murawala/Dunja Knapp GFP-labeled LPM was transplanted to a white-host embryo. The limb of the host was amputated and the blastema sample was collected.
LPM-transplant Blastema samples of a LPM-transplanted animal: mature and 7dpa Blastema Single-ended 180bp FastQ LPM/An7.fastq.tar.gz Prayag Murawala/Dunja Knapp GFP-labeled LPM was transplanted to a white-host embryo. The limb of the host was amputated and the blastema sample was collected.
LPM-transplant Blastema samples of a LPM-transplanted animal: mature and 3dpa Blastema Single-ended 180bp FastQ LPM/An8.fastq.tar.gz Prayag Murawala/Dunja Knapp GFP-labeled LPM was transplanted to a white-host embryo. The limb of the host was amputated and the blastema sample was collected.

Unsorted Illumina data can be found under //biodata/groups/crtd_tanaka/LabData/Sequencing/Illumina.

Sanger

The data can be found under //biodata/groups/crtd_tanaka/LabData/Sequencing/Sanger.

Name Description Tissue Sequences Location Author Remarks
LimbBlastema Limb blastema library Limb blastema 20160 (RSD) / 15648 (SCF)
  • SCF files: LimbBlastema/LB_SCF.gz
  • RSD files: LimbBlastema/LB_RSD.gz
 Akira Tazaki
NeuraTube Neural tube library Teural tube 4896 (RSD) / 7905 (SCF)
  • SCF files: NeuralTube/NT_SCF.gz
  • RSD files: NeuralTube/NT_RSD.gz
 Akira Tazaki

Roche/454

The data can be found under //biodata/groups/crtd_tanaka/LabData/Sequencing/454.

Name Description Tissue Reads Format Location Author Remarks
454 Mixed 454 Mixed 1,208,954 Fasta/Qual Ax_454.tar.gz n/a

Microarrays

The data can be found under //biodata/groups/crtd_tanaka/LabData/Microarrays. Also consult the file Contents.txt in the experiment directory for more details. The raw data (*.tiff) files can be found in the subdirectory Raw in the experiment directory.

Name Description Timepoints Tissue Array type Location Author 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
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 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 Dunja Knapp
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