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GEO help: Mouse over screen elements for information. |
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| Status |
Public on May 19, 2024 |
| Title |
Sort-purified (CD8/CD45.1) TCR OT1 CD8 T cells from B16-OVA-GP61 tumors (no TCR SMARTA CD4 T cells) replicate#2 [ATAC] |
| Sample type |
SRA |
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| Source name |
tumor
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| Organism |
Mus musculus |
| Characteristics |
tissue: tumor
cell line: B16-OVA-GP61
cell type: CD8 T cell
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
CD8 T cells were FACS-sorted into FCS containing tubes and after sort 10% DMSO were added, mixed and stored at -80°C until all samples were collected. Profiling of Chromatin was performed by ATAC-seq. Cells were thawed and washed in cold PBS and lysed.
After cell lysis, transposition happened at 42ºC for 45 min. After purification of the DNA with the MinElute PCR purification kit (Qiagen), material was amplified for 5 cycles. Additional PCR cycles were evaluated by real time PCR. Final product was cleaned by Ampure Beads at a 1.5x ratio. Libraries were sequenced on a Hiseq 2500 1T in a 50bp/50bp Paired end run, using the TruSeq SBS Kit v3 (Illumina). An average of 47x106 paired reads were generated per sample.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Reads were aligned to the mouse reference genome (version GRCm38) with BWA-backtrack v0.7.17 (Li and Durbin, 2009).
Post-alignment filtering was done with samtools v1.8 and Picard tools v2.18.9 (Li et al., 2009) to remove unmapped reads, improperly paired reads, nonunique reads, and duplicates.
Peaks were called with MACS2 v2.1.1 (Liu, 2014),and peaks with adjusted P values smaller than 0.01 were excluded.
Consensus peak sets were generated for each condition if a peak was found in at least two replicates.
Reproducible peaks from each condition were merged with DiffBind v3.4.11 to create an atlas of accessible peaks, which was used for downstream analyses.
Assembly: GRCm38
Supplementary files format and content: bigWig, narrowPeak
Supplementary files format and content: tab-delimted file containing raw counts per peak per sample
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| Submission date |
Apr 25, 2024 |
| Last update date |
May 20, 2024 |
| Contact name |
Andrea Schietinger |
| Organization name |
Memorial Sloan Kettering Cancer Center
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| Department |
Immunology
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| Street address |
1275 York Avenue
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
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| Platform ID |
GPL17021 |
| Series (1) |
| GSE265847 |
The role of CD4 T cells in tumor-specific CD8 T cell reprogramming [ATAC-Seq] |
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| Relations |
| BioSample |
SAMN41082927 |
| SRA |
SRX24368349 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8230004_O2A_PF.narrowPeak.gz |
1.7 Mb |
(ftp)(http) |
NARROWPEAK |
| GSM8230004_O2A_normTo1x.bw |
411.9 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
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