|
| Status |
Public on Jan 15, 2020 |
| Title |
FSF_epi_3 |
| Sample type |
SRA |
| |
|
| Source name |
axolotl limb
|
| Organism |
Ambystoma mexicanum |
| Characteristics |
tissue: Axolotl limb
cell population: Epithelial cells of full thickness skin
time point: 5 days post-amputation (dpa)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Regenerating tissue was isolated from limbs at 5 dpa. Epidermis and stump tissues were separate dissociated, DAPI stained, and FACS sorted based on cell cycle content. RNA was extracted using the RecoverAll Total Nucleic Acid Isolation Kit for FFPE. More details can be found in Tsai et al. (2019).
cDNA was synthesized with the NuGEN Ovation RNA-seq System V2, mechanically sheared to approximately 200 bp, and libraries were prepped using the Wafergen PrepX Complete ILMN DNA Library kit and the Apollo 324 NGS Library Prep System.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Mexican axolotl
processed data file: matrix.TMM.EXPR.matrix
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Adapters and reads were trimmed using Trimmomatic to a minimum length of 100 bp and aligned to the axolotl transcriptome from Whited et al. (2017) using Kallisto.
Un-normalized counts were fed into DESeq2 for differential expression analysis.
Genome_build: axolotl transcriptome (Whited et al. 2017)
Supplementary_files_format_and_content: matrix.TMM.EXPR.matrix: Tab-delimited text file includes TMM-normalized TPM values for each sample.
|
| |
|
| Submission date |
Jun 06, 2019 |
| Last update date |
Jan 15, 2020 |
| Contact name |
Douglas A. Melton |
| E-mail(s) |
dmelton@harvard.edu
|
| Organization name |
Harvard University
|
| Street address |
7 Divinity Ave.
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02138 |
| Country |
USA |
| |
|
| Platform ID |
GPL22800 |
| Series (1) |
| GSE132317 |
Wound epidermis-dependent transcriptional programs |
|
| Relations |
| BioSample |
SAMN11970044 |
| SRA |
SRX5982656 |
