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Sample GSM8121002

Query DataSets for GSM8121002

Status

Public on Mar 26, 2024

Title

wild-type atRA+PKCi HFSCs 1, ATAC-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: wild-type
treatment: atRA+PKCi

Extracted molecule

genomic DNA

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, cells were pelleted, lysed, and processed as described in Buenrostro et al., 2013.
Libraries were prepared according to the manufacturer’s guidelines (Illumina). Briefly cells were transposed with Tn5 transposase for 30 min and samples were barcoded.

Library strategy

ATAC-seq

Library source

genomic

Library selection

other

Instrument model

Illumina NovaSeq 6000

Description

ATAC-seq

Data processing

50 bp paired-end FASTQs were aligned to the mouse genome (mm10) using the Bowtie (v.1.1.2). Aligned reads were de-duplicated with Picard (v.2.3.0; Broad Institute, 2019) and shifted to correct for Tn5 insertion bias. Peaks were called using MACS2 (v.2.1.1), concatenated to a union peak set, and the read coverage of each sample at these peaks was calculated with Bedtools (v.2.25).
Assembly: mm10
Supplementary files format and content: Bedfiles of peaks called using MACS2 (v.2.1.1).

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