|
| Status |
Public on May 26, 2022 |
| Title |
in vitro TEX day 8 replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
primary CD8 T cells
|
| Organism |
Mus |
| Characteristics |
cell type: primary CD8 T cells
days of_anti-cd3_stim: 6
sgrna: None
sgrna delivery: NA
|
| Treatment protocol |
After activation, T cells were plated on chronic stimulation (anti-CD3 coated) plates to induce exhaustion
|
| Growth protocol |
Primary T cells were isolated from mouse spleen or human blood and cultured in media containing IL-2
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Live CD8+ T cells were isolated by FACS and subjected to ATAC-seq
Omni ATAC-seq was performed as previously described (Corces et al Nature Methods 2017)
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Reads were trimmed and quality filtered using fastp.
Reads were aligned to mm10 or hg38 using hisat2
Aligned reads were de-duplicated using Picard
Mitochondrial reads and Y chromosome reads were removed
Peaks were called for each sample using MACS2, merged into a union peak set, and the peak by count matrix was loaded into DESeq2 for differential analysis
Assembly: mm10 or hg38
Supplementary files format and content: Genome tracks files were created by using the deduplicated reads, normalizing each sample using counts in TSS, and exported from R as bigwig files.
|
| |
|
| Submission date |
May 23, 2022 |
| Last update date |
May 27, 2022 |
| Contact name |
Julia Belk |
| Organization name |
Stanford University
|
| Street address |
450 Serra Mall
|
| City |
Stanford |
| State/province |
California |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL31136 |
| Series (2) |
| GSE203591 |
Genome-wide CRISPR screens of T cell exhaustion identify chromatin remodeling factors that limit T cell persistence [ATAC-seq] |
| GSE203593 |
Genome-wide CRISPR screens of T cell exhaustion identify chromatin remodeling factors that limit T cell persistence |
|
| Relations |
| BioSample |
SAMN28597482 |
| SRA |
SRX15414587 |
