|
| Status |
Public on Nov 05, 2023 |
| Title |
13_19_none |
| 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: none
|
| 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 |
SAMN38083780 |
| SRA |
SRX22359760 |
