|
| Status |
Public on Sep 30, 2021 |
| Title |
Bulk_HFSC1 |
| Sample type |
SRA |
| |
|
| Source name |
HFSC
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: back skin
age: Post natal day 30
|
| Treatment protocol |
K14Cre mediated Foxc1 Nfatc1 double knockout and control epidermal cells
|
| Extracted molecule |
genomic DNA |
| 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.
For bulk HFSC ATACseq, we were following Nextera DNA Sample Preparation Kit, Illumina. For single cell ATACseq, we use 10xgenomics single cell ATACseq protocol.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
ATAC
|
| Data processing |
Fastq files were acquired from illumina sequencing facility
For bulk ATACseq, the reads were mapped to mouse genome using bowtie2 with paratmeters -p 18 -q --local. Then we remove the mitochondrial DNA. The sam files were then converted to bamfiles. After we remove duplicates from sorted and indexed bamfiles, peak calling was done by macs2 with parameters -f BAM -g mm --nomodel -q 1e-5.
For single cell ATACseq, the reads were processed using cell ranger atac mm10 1.0.1
Genome_build: mm10
Supplementary_files_format_and_content: Peak file and fragment 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) |
| GSE133646 |
Open chromatin analysis of hair follcile stem cell quiescence |
| GSE133648 |
Escape of hair follicle stem cells from a defective niche |
|
| Relations |
| BioSample |
SAMN12175175 |
| SRA |
SRX6386847 |
