Antitumor progenitor exhausted CD8 T cells are sustained with TCR engagement [ATACseq]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 24 samples
- What it is
- ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
- Organism
- Mus musculus (mouse)
- Samples
- 24 samples: 24 samples, each with a distinct title — no replicated groupsGroups are read from the sample names, not from the paper. Check the list below.
- Data you can get
- A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
- Paper
- Antitumor progenitor exhausted CD8(+) T cells are sustained by TCR engagementNature immunology · 2024
Read the full summary ↓
Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.
Processed table
The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE262842_RAW.tar (it can run to tens of gigabytes).
Raw sequencing reads
The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.
What the files usually look like: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.
Also filed as BioProject PRJNA1093468 and SRA study SRP498766. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 24 sample titles: 24 distinct titles with little repetition. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.
- GSM8180280 Naive, replicate 1, ATAC
- GSM8180281 Naive, replicate 2, ATAC
- GSM8180282 M9_LN, replicate 1, ATAC
- GSM8180283 C6M9_LN, replicate 1, ATAC
- GSM8180284 M9_TU_Tpex, replicate 1, ATAC
- GSM8180285 M9_LN, replicate 2, ATAC
- GSM8180286 M9_TU_Tpex, replicate 2, ATAC
- GSM8180287 M9_LN, replicate 3, ATAC
- GSM8180288 C6M9_LN, replicate 2, ATAC
- GSM8180289 M9_TU_Tpex, replicate 3, ATAC
- GSM8180290 M9_TU_Tex, replicate 1, ATAC
- GSM8180291 C6M9_TU_Tpex, replicate 1, ATAC
- GSM8180292 C6M9_TU_Tex, replicate 1, ATAC
- GSM8180293 M9_LN, replicate 4, ATAC
- GSM8180294 C6M9_LN, replicate 3, ATAC
- GSM8180295 M9_TU_Tpex, replicate 4, ATAC
- GSM8180296 M9_TU_Tex, replicate 2, ATAC
- GSM8180297 C6M9_TU_Tpex, replicate 2, ATAC
- GSM8180298 C6M9_TU_Tex, replicate 2, ATAC
- GSM8180299 M9_TU_Tpex, replicate 5, ATAC
- GSM8180300 C6M9_TU_Tpex, replicate 3, ATAC
- GSM8180301 C6M9_LN, replicate 4, ATAC
- GSM8180302 C6M9_TU_Tpex, replicate 4, ATAC
- GSM8180303 C6M9_TU_Tpex, replicate 5, ATAC
- GSE304763 A pan-immunotherapy signature to predict intratumoral CD8+ T cell expansions [scTCR_immunotherapies] 91 samples shares cd8, tcr
- GSE235005 Nutrient-driven histone code determines exhausted CD8+ T cell fates [ChIP-seq] 50 samples shares cd8, exhausted
- GSE337898 ATAC-seq profiling of lineage-traced exhausted and memory-like CD8+ T cell subsets during tumor progression 24 samples shares cd8, exhausted
- GSE276300 EGR2 O-GlcNAcylation Orchestrates the Development of Protumoral Macrophages to Limit CD8+ T Cell Antitumor Responses. 27 samples shares cd8, antitumor
- GSE285187 A core stemness program in exhausted CD8+ T cells 24 samples shares cd8, exhausted
- GSE261642 PLPP1-deficiency-mediated ferroptosis induced by PD-1 signaling impairs antitumor activity of intratumoral CD8+ T cells I 23 samples shares cd8, antitumor
- GSE285414 Functional memory T cells are derived from exhausted clones and expanded by checkpoint blockade [scRNATCR_rechallenge] 21 samples shares tcr, exhausted
- GSE299133 Host MTDH orchestrates liver lipid metabolism and CD8+ T cells to suppress antitumor immunity [Hepatocytes] 18 samples shares cd8, antitumor
Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.