|
Status |
Public on Nov 05, 2023 |
Title |
14_20_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).
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|
|
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
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|
|
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 |
SAMN38083779 |
SRA |
SRX22359762 |