|
| Status |
Public on Mar 26, 2024 |
| Title |
Rxra cKO atRA+PKCi HFSCs 1, RNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
Telogen (P55) skin mouse 1
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Telogen (P55) skin mouse 1
cell type: Hair follicle stem cells
genotype: Rxra cKO
treatment: atRA+PKCi
|
| Extracted molecule |
total RNA |
| Extraction protocol |
To resuspend HFSCs, 3D cultures were washed with sterile PBS, dissociated into single cell suspensions using TrpLE-Express (Gibco) for 15min at 37°C. After filtering, total RNA was collected in Trizol and purified using the Direct-zol RNA MiniPrep kit (Zymo Research) according to the manufacturer's instructions. DNase treatment was performed to remove genomic DNA (RNase-Free DNase Set, Qiagen). Sample quality was determined using an Agilent 2100 Bioanalyzer; all samples for sequencing had RNA integrity (RIN) numbers >8.
cDNA library construction was performed by the Rockefeller University (RU) Genomic Core facility.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
KO_RA_1
|
| Data processing |
Transcript abundance was quantified using Salmon (v.1.4.0) with a reference genome sequence fetched from BSGenome.Mmusculus.UCSC.mm10 package. Gene level counts and transcripts per million (TPM) were calculated using Tximport (v.1.12.3) package.
Assembly: mm10
Supplementary files format and content: Tab-delineated text files or comma separated value files contain raw counts.
|
| |
|
| Submission date |
Feb 29, 2024 |
| Last update date |
Mar 26, 2024 |
| Contact name |
Matthew T Tierney |
| E-mail(s) |
[email protected]
|
| Phone |
5857974876
|
| Organization name |
Rockefeller University
|
| Street address |
1230 York Ave, Box 300
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE231731 |
Retinoic acid promotes tissue regeneration by resolving stem cell lineage plasticity |
|
| Relations |
| BioSample |
SAMN40207200 |
| SRA |
SRX23799349 |
