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Status |
Public on Jun 13, 2023 |
Title |
WT cells, 48h activated in vitro; IL-12 [IL-12_Rep1] |
Sample type |
SRA |
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Source name |
WT
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Organism |
Mus musculus |
Characteristics |
cell line: WT cell type: CD8+ treatment: IL-12
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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.
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Library strategy |
ATAC-seq |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina NextSeq 500 |
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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
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Submission date |
Mar 24, 2023 |
Last update date |
Jun 13, 2023 |
Contact name |
Bryan McDonald |
E-mail(s) |
bmcdonald@salk.edu
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Organization name |
Salk Institute for Biological Studies
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Street address |
10010 N Torrey Pines Rd
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City |
San Diego |
State/province |
CA |
ZIP/Postal code |
92037 |
Country |
USA |
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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 |
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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 Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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