Datasets: Difference between revisions
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== Sequences == | == Sequences == | ||
=== Illumina === | === Illumina === | ||
The data can be found under <b>//biodata/groups/ | 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 149: | Line 149: | ||
|LPM-transplant | |LPM-transplant | ||
|Blastema samples of a LPM-transplanted animal: mature and 1dpa | |Blastema samples of a LPM-transplanted animal: mature and 1dpa | ||
| | |Limb blastema | ||
|Single-ended | |Single-ended | ||
| | | | ||
|180bp | |180bp | ||
| | |<ul><li>Mature: 35,982,029</li><li>1dpa: 39,824,276</li></ul> | ||
|FastQ | |FastQ | ||
|LPM/An3.fastq.tar.gz | |LPM/An3.fastq.tar.gz | ||
| Line 161: | Line 161: | ||
|LPM-transplant | |LPM-transplant | ||
|Blastema samples of a LPM-transplanted animal: mature and 10dpa | |Blastema samples of a LPM-transplanted animal: mature and 10dpa | ||
| | |Limb blastema | ||
|Single-ended | |Single-ended | ||
| | | | ||
|180bp | |180bp | ||
| | |<ul><li>Mature: 47,155,937</li><li>10dpa: 40,468,959</li></ul> | ||
|FastQ | |FastQ | ||
|LPM/An4.fastq.tar.gz | |LPM/An4.fastq.tar.gz | ||
| Line 173: | Line 173: | ||
|LPM-transplant | |LPM-transplant | ||
|Blastema samples of a LPM-transplanted animal: mature and 5dpa | |Blastema samples of a LPM-transplanted animal: mature and 5dpa | ||
| | |Limb blastema | ||
|Single-ended | |Single-ended | ||
| | | | ||
| Line 185: | Line 185: | ||
|LPM-transplant | |LPM-transplant | ||
|Blastema samples of a LPM-transplanted animal: mature and 7dpa | |Blastema samples of a LPM-transplanted animal: mature and 7dpa | ||
| | |Limb blastema | ||
|Single-ended | |Single-ended | ||
| | | | ||
|180bp | |180bp | ||
| | |<ul><li>Mature: 52,385,146</li><li>7dpa: 54,639,187</li></ul> | ||
|FastQ | |FastQ | ||
|LPM/An7.fastq.tar.gz | |LPM/An7.fastq.tar.gz | ||
| Line 197: | Line 197: | ||
|LPM-transplant | |LPM-transplant | ||
|Blastema samples of a LPM-transplanted animal: mature and 3dpa | |Blastema samples of a LPM-transplanted animal: mature and 3dpa | ||
| | |Limb blastema | ||
|Single-ended | |Single-ended | ||
| | | | ||
|180bp | |180bp | ||
| | |<ul><li>Mature: 69,327,682</li><li>3dpa: 52,633,592</li></ul> | ||
|FastQ | |FastQ | ||
|LPM/An8.fastq.tar.gz | |LPM/An8.fastq.tar.gz | ||
| Line 208: | Line 208: | ||
|} | |} | ||
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/ | 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 | ||
| Line 231: | Line 232: | ||
|NeuraTube | |NeuraTube | ||
|Neural tube library | |Neural tube library | ||
| | |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 239: | Line 240: | ||
=== Roche/454 === | === Roche/454 === | ||
The data can be found under <b>//biodata/groups/ | 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 | ||
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 |
|
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 |
|
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 |
|
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 |
|
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 |
|
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) |
|
Akira Tazaki | |
| NeuraTube | Neural tube library | Neural tube | 4896 (RSD) / 7905 (SCF) |
|
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 |