Datasets

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