Datasets
Sequences
Illumina
The data can be found under //biodata/groups/crtd_tanaka/LabData/Sequencing/Illumina.
| Name | Description | Tissue | Type | Read length | Reads | Format | Location | Author | 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 | |
| LPM-transplant | Blastema samples of a LPM-transplanted animal: mature and 1dpa | Blastema | Single-ended | 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 | 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 | 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 | 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 | 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) |
|
Akira Tazaki | |
| NeuraTube | Neural tube library | Teural tube | 4896 (RSD) / 7905 (SCF) |
|
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 |