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Series GSE133646 Query DataSets for GSE133646
Status Public on Sep 30, 2021
Title Open chromatin analysis of hair follcile stem cell quiescence
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Tissue stem cells are required for homeostasis and wound repair throughout the entire lifespan. Multiple mechanisms have been extensively studied for the maintenance of stem cell quiescence. Here we use Omini-ATACseq and single cell ATACseq to study the stem cell quiescence at epigenetic level. We sought out to compare the open chromatin state in different cell lineages between control and Foxc1/Nfatc1 double knockout mice. The single cell ATACseq could further help infer the transcription regulation between enhancers and promoters interaction.
Overall design For the bulk omini ATACseq, all the hair follicle stem cells(HFSCs) were FACS sorted and used to perform omini-ATACseq assay. For single cell ATACseq, the epidermal cells were sorted such that the interfollicular epidermis and hair follicle cells were at the ratio of 1:3. A total of 10k cells were collected and used for the assay. We followed the 10xgenomics single cell ATACseq protocol.
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Contributor(s) Zhang C
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Submission date Jul 01, 2019
Last update date Nov 02, 2021
Contact name Chi Zhang
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
Platforms (1)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (4)
GSM3914151 Bulk_HFSC1
GSM3914152 Bulk_HFSC2
GSM3914153 Ctrl_scATAC
This SubSeries is part of SuperSeries:
GSE133648 Escape of hair follicle stem cells from a defective niche
BioProject PRJNA552095
SRA SRP212731

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE133646_RAW.tar 3.5 Gb (http)(custom) TAR (of BED, CSV, TSV)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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