|
| Status |
Public on Sep 30, 2021 |
| Title |
Nfatc1 Ctrl2 |
| Sample type |
SRA |
| |
|
| Source name |
Back skin hair follicle
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: back skin
age: Post natal day 30
|
| Treatment protocol |
For K15CrePR samples, mice were treated with tamoxifen for 6 days from P22 till P28 and then collect samples at P30.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Mice at appropiate age were euthenized. Back skin is dissectd and digested with Collagenase and Trypsin to get single cell suspension. HFSCs were sorted based on specific cell surface markers and endogenous fluorescent markers.
NEBNext® Ultra™ Directional RNA Library Prep Kit is used for library construction.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Fastq files were acquired from illumina sequencing facility
Sequencing reads were tirmmed for adaptors and test quanlity with fastqc. The trimmed reads were then mapped to mouse genome mm10 using hisat2 with parameters -p 32 --rna-strandness RF
The mapped sam files were then converted to bam files, then sorted and indexed.
The sorted bam files were then counted using htseq-count with parameter -t exon -i gene_id --stranded=reverse -f bam
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited count file
|
| |
|
| Submission date |
Jul 01, 2019 |
| Last update date |
Sep 30, 2021 |
| Contact name |
Chi Zhang |
| E-mail(s) |
chzh1418@colorado.edu
|
| Organization name |
University of Colorado Boulder
|
| Department |
MCDB
|
| Lab |
Yi Rui Lab
|
| Street address |
347 UCB
|
| City |
Boulder |
| State/province |
Colorado |
| ZIP/Postal code |
80309 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE133647 |
Transcriptome analysis of hair follcile stem cell quiescence |
| GSE133648 |
Escape of hair follicle stem cells from a defective niche |
|
| Relations |
| BioSample |
SAMN12175163 |
| SRA |
SRX6386854 |
