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Sample GSM7881005 Query DataSets for GSM7881005
Status Public on Nov 05, 2023
Title 16_18_TGFb
Sample type SRA
 
Source name lymphoid organs (lymph nodes and spleen)
Organism Mus musculus
Characteristics tissue: lymphoid organs (lymph nodes and spleen)
cell type: FACS: Live/Dead -, CD45.1+, CD8a+ (OT-I T cells)
time: 2h
treatment: TGFb
Treatment protocol Cells were cultured in conditions of 2 hours no stimulation, 2 hours stimulation with 100ng/mL TGF-β, 24 hours stimulation with 100nM N4 (SIINFEKL), and 24 hours stimulation with 100nM N4 (SIINFEKL) and 100ng/mL TGF-β.
Growth protocol To enrich bulk T cells from single cell suspensions, we used a mouse-specific T cell negative isolation MACS (STEMCELL Technologies, Canada). We plated 0.5–1 × 106 T cells per well in 96-well V-bottom tissue culture plates. We cultured cells in mouse RP10 media (RPMI 1640 supplemented with 10% FBS, 2mM L-glutamine, 100 U/mL penicillin-streptomycin, 1mM sodium pyruvate, 0.05mM β mercaptoethanol, and 1mM HEPES) at 37°C with 5% CO2.
Extracted molecule genomic DNA
Extraction protocol ATAC-seq was performed on pools of 40,000 to 50,000 sort-purified OT-I T cells pooled from 2 to 3 mice. Extraction and library constuction was performed according to (Buenrostro JD et. al 2015, https://doi.org/10.1002/0471142727.mb2129s109).
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model NextSeq 2000
 
Description bulk ATACseq
Data processing Fastq data processed with ENCODE ATAC-seq pipeline v1.7 except MACS2 input limited to a maximum 50 million mapped reads per replicate
MACS2 output for each replicate was filtered for peaks with q-value less than 0.0001
Bedtools merge was used to consolidate peaks from all replicates to a common peak set
Peaks were resized to a uniform size of 500 bp
Reads overlapping peaks were computed for all replicates and normalized with limma/voom
Peaks limited to those with a mean of at least 6 normalized counts per million mapped reads in at least 1 biological group
Assembly: GRCm38
Supplementary files format and content: tab-seperated values containing voom normalized ATAC-seq counts per peak
 
Submission date Nov 02, 2023
Last update date Nov 05, 2023
Contact name Martin Prlic
E-mail(s) mprlic@fredhutch.org
Phone 2066672216
Organization name Fred Hutchinson Cancer Center
Lab Prlic
Street address 1100 Fairview Ave, Mail stop E5-110
City Seattle
State/province WA
ZIP/Postal code 98102
Country USA
 
Platform ID GPL30172
Series (2)
GSE246930 TGF-β broadly modifies rather than specifically suppresses reactivated memory CD8 T cells in a dose-dependent manner (ATAC-Seq)
GSE246933 TGF-β broadly modifies rather than specifically suppresses reactivated memory CD8 T cells in a dose-dependent manner
Relations
BioSample SAMN38083781
SRA SRX22359758

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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