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Sample GSM7116306 Query DataSets for GSM7116306
Status Public on Jun 13, 2023
Title WT cells, 48h activated in vitro; IL-12 [IL-12_Rep1]
Sample type SRA
 
Source name WT
Organism Mus musculus
Characteristics cell line: WT
cell type: CD8+
treatment: IL-12
Extracted molecule genomic DNA
Extraction protocol Cells were lysed in RSB (10mM Tris-HCl (pH 7.4), 10mM NaCl, 3mM MgCl2, 0.1% NP-40) supplemented with 0.1% Tween-20, and 0.01% digitonin for 3 minutes on ice and then washed with RSB supplemeneted with 0.1% Tween-20
Nuclei were then transposed for 30min at 37C with 1000RPM mixing in 50uL transposition mix (25uL 2X TD buffer, 2.5uL Tn5 transposase (100nM final), 16uL PBS, 0.5uL 1% digitonin, 0.5uL 10% Tween-20, 5uL H2O)
DNA was purified with Qiagen MinElute PCR cleanup kit. Libraries were amplified after determining the optimal number of cycles by qPCR. Post amplification libraries were size selected using Agencourt AMPure XP beads from Beckman Coulter.
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina NextSeq 500
 
Data processing Sequence reads were aligned to GRCm38 (mm10) using STAR v2.5.3a (parameters- default)
ATAC-seq peaks were identified using the findPeaks program in HOMER with the following options "-style dnase -o auto"
Assembly: GRCm38 (mm10)
Supplementary files format and content: bigwig, bed
 
Submission date Mar 24, 2023
Last update date Jun 13, 2023
Contact name Bryan McDonald
E-mail(s) bmcdonald@salk.edu
Organization name Salk Institute for Biological Studies
Street address 10010 N Torrey Pines Rd
City San Diego
State/province CA
ZIP/Postal code 92037
Country USA
 
Platform ID GPL19057
Series (2)
GSE228193 Effect of BAF disruption on chromatin accessibility in activated CD8+ T cells [ATAC-seq]
GSE228381 Canonical BAF complex activity shapes the enhancer landscape that licenses CD8+ T cell effector and memory fates
Relations
BioSample SAMN33906418
SRA SRX19767394

Supplementary file Size Download File type/resource
GSM7116306_DMSO_ILL2_Rep1.bw 204.1 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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