Datasets: Difference between revisions

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== Sequences ==
== Sequences ==
=== Illumina ===
=== Illumina ===
The data can be found under <b>//biodata/groups/crtd_tanaka/LabData/Sequencing/Illumina</b>.
The data can be found under <b>//biodata/groups/axolotl-transcriptome/raw/Illumina</b>.
         {| class="wikitable sortable"
         {| class="wikitable sortable"
         !style="width: 200px" class="unsortable" | Name
         !style="width: 200px" class="unsortable" | Name
Line 8: Line 8:
         !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"                    | Reads
         !style="width: 100px"  class="unsortable"| Fragment size
        !style="width: 150px"                    | Reads
         !style="width: 100px" class="unsortable" | Format
         !style="width: 100px" class="unsortable" | Format
         !style="width: 200px" class="unsortable" | Location
         !style="width: 200px" class="unsortable" | Location
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         |Paired-ended
         |Paired-ended
         |100bp
         |100bp
        |200-250bp
         |65,753,941
         |65,753,941
         |FastQ
         |FastQ
Line 30: Line 32:
         |Paired-ended
         |Paired-ended
         |100bp
         |100bp
        |200-250bp
         |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
Line 52: Line 56:
         |Paired-ended
         |Paired-ended
         |100bp
         |100bp
        |180bp
         |95,946,545
         |95,946,545
         |FastQ
         |FastQ
Line 63: Line 68:
         |Paired-ended
         |Paired-ended
         |100bp
         |100bp
        |180bp
         |96,626,387
         |96,626,387
         |FastQ
         |FastQ
Line 74: Line 80:
         |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
Line 96: Line 104:
         |Single-ended
         |Single-ended
         |76bp
         |76bp
        |n/a
         |65,250,768
         |65,250,768
         |FastQ
         |FastQ
Line 107: Line 116:
         |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
Line 134: Line 146:
         |Dunja Knapp
         |Dunja Knapp
         |
         |
        |-
        |LPM-transplant
        |Blastema samples of a LPM-transplanted animal: mature and 1dpa
        |Limb blastema
        |Single-ended
        |
        |180bp
        |<ul><li>Mature: 35,982,029</li><li>1dpa: 39,824,276</li></ul>
        |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
        |Limb blastema
        |Single-ended
        |
        |180bp
        |<ul><li>Mature: 47,155,937</li><li>10dpa: 40,468,959</li></ul>
        |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
        |Limb blastema
        |Single-ended
        |
        |180bp
        |<ul><li>Mature: 38,879,295</li><li>5dpa: 33,775,319</li></ul>
        |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
        |Limb blastema
        |Single-ended
        |
        |180bp
        |<ul><li>Mature: 52,385,146</li><li>7dpa: 54,639,187</li></ul>
        |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
        |Limb blastema
        |Single-ended
        |
        |180bp
        |<ul><li>Mature: 69,327,682</li><li>3dpa: 52,633,592</li></ul>
        |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 <b>//biodata/groups/crtd_tanaka/LabData/Sequencing/Illumina</b>.
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>.


=== Sanger ===
=== Sanger ===
The data can be found under <b>//biodata/groups/crtd_tanaka/LabData/Sequencing/Sanger</b>.
The data can be found under <b>//biodata/groups/axolotl-transcriptome/raw/Sanger</b>.
         {| class="wikitable sortable"
         {| class="wikitable sortable"
         !style="width: 200px" class="unsortable" | Name
         !style="width: 200px" class="unsortable" | Name
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         |NeuraTube
         |NeuraTube
         |Neural tube library
         |Neural tube library
         |Teural tube
         |Neural tube
         |4896 (RSD) / 7905 (SCF)
         |4896 (RSD) / 7905 (SCF)
         |<ul><li>SCF files: NeuralTube/NT_SCF.gz</li><li>RSD files: NeuralTube/NT_RSD.gz</li></ul>
         |<ul><li>SCF files: NeuralTube/NT_SCF.gz</li><li>RSD files: NeuralTube/NT_RSD.gz</li></ul>
Line 167: Line 240:


=== Roche/454 ===
=== Roche/454 ===
The data can be found under <b>//biodata/groups/crtd_tanaka/LabData/Sequencing/454</b>.
The data can be found under <b>//biodata/groups/axolotl-transcriptome/raw/454</b>.
         {| class="wikitable"
         {| class="wikitable"
         !style="width: 200px" | Name
         !style="width: 200px" | Name
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         |Agilent, 44000
         |Agilent, 44000
         |Fin_vs_bulk
         |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
         |Eugeniu Nacu
         |
         |
Line 226: Line 290:
         |
         |
         |-
         |-
         |Limb timecourse 2
         |Limb timecourse
         |Timecourse microarray experiment using limb
         |Timecourse microarray experiment using limb
         |0, 3h, 6h, 9h, 12h, 24h, 36h, 52h, 72h, 120h, 168h, 288h, 528h
         |0, 3h, 6h, 9h, 12h, 24h, 36h, 52h, 72h, 120h, 168h, 288h, 528h
         |Mature limb and limb bud
         |Mature limb and limb bud
         |Agilent, 44000
         |Agilent, 44000
         |Limb_timecourse_2
         |Limb_timecourse
         |Dunja Knapp
         |Dunja Knapp
         |
         |
         |}
         |}

Latest revision as of 16:43, 30 June 2013

Sequences

Illumina

The data can be found under //biodata/groups/axolotl-transcriptome/raw/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 200-250bp 65,753,941 FastQ SpinalCord/mSC.fastq.tar.gz Akira Tazaki
Injured spinal cord Injured axolotl spinal cord, 6dpi Spinal cord Paired-ended 100bp 200-250bp 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 Limb blastema Single-ended 180bp
  • Mature: 35,982,029
  • 1dpa: 39,824,276
 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 Limb blastema Single-ended 180bp
  • Mature: 47,155,937
  • 10dpa: 40,468,959
 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 Limb blastema Single-ended 180bp
  • Mature: 38,879,295
  • 5dpa: 33,775,319
 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 Limb blastema Single-ended 180bp
  • Mature: 52,385,146
  • 7dpa: 54,639,187
 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 Limb blastema Single-ended 180bp
  • Mature: 69,327,682
  • 3dpa: 52,633,592
 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/unsorted.
For some of the data sets quality check was performed using FastQC. The statistics can be found under //biodata/groups/crtd_tanaka/LabData/Sequencing/Illumina/qualitycheck.

Sanger

The data can be found under //biodata/groups/axolotl-transcriptome/raw/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 Neural 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/axolotl-transcriptome/raw/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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