Deletion of a state-specific PD-1 enhancer modulates exhausted T cell fate and function [ATAC-seq]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 12 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
- 12 samples: 12 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
- Epigenetic tuning of PD-1 expression improves exhausted T cell function and viral controlNature 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 GSE212506_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 PRJNA875661 and SRA study SRP395211. 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 12 sample titles: 12 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.
- GSM6533800 Pdcd1 EnhDel terminally exhausted CD8+ T cells, replicate 1, ATACseq
- GSM6533801 Pdcd1 EnhDel progenitor exhausted CD8+ T cells, replicate 1, ATACseq
- GSM6533802 Pdcd1 EnhDel terminally exhausted CD8+ T cells, replicate 2, ATACseq
- GSM6533803 Pdcd1 EnhDel progenitor exhausted CD8+ T cells, replicate 2, ATACseq
- GSM6533804 PD-1 KO terminally exhausted CD8+ T cells, repilcate 1, ATACseq
- GSM6533805 PD-1 KO progenitor exhausted CD8+ T cells, replicate 1, ATACseq
- GSM6533806 PD-1 KO terminally exhausted CD8+ T cells, replicate 2, ATACseq
- GSM6533807 PD-1 KO progenitor exhausted CD8+ T cells, replicate 2, ATACseq
- GSM6533808 Wild type terminally exhausted CD8+ T cells, replicate 1, ATACseq
- GSM6533809 Wild type progenitor exhausted CD8+ T cells, replicate 1, ATACseq
- GSM6533810 Wild type terminally exhausted CD8+ T cells, replicate 2, ATACseq
- GSM6533811 Wild type progenitor exhausted CD8+ T cells, replicate 2, ATACseq
- GSE320007 Distinct Stemness Programs and PD-1 Responsiveness of Progenitor Exhausted CD8+ T Cells between Chronic Viral Infection and Tumor 10 samples shares pd-1, exhausted
- GSE235005 Nutrient-driven histone code determines exhausted CD8+ T cell fates [ChIP-seq] 50 samples shares exhausted, fate
- GSE310322 Mapping self-associating chromatin hubs identifies Id proteins as key determinants of exhausted T cell fate 37 samples shares exhausted, fate
- GSE285308 Functional memory T cells are derived from exhausted clones and expanded by checkpoint blockade [ATAC-Seq] 33 samples shares exhausted, atac-seq
- GSE337898 ATAC-seq profiling of lineage-traced exhausted and memory-like CD8+ T cell subsets during tumor progression 24 samples shares exhausted, atac-seq
- GSE280128 The LHX1 Gene Regulatory Network Represses Pluripotency and Modulates Multiple Signaling Pathways to Specify the Embryonic Head [Embryo_ATAC-seq] 12 samples shares modulates, atac-seq
- GSE288039 Krüppel-like factor 2 programs early exhausted T cell states and restrains antiviral immunity [ATAC-seq] 12 samples shares exhausted, atac-seq
- GSE248534 Lamin A/C-regulated cysteine catabolic flux modulates stem cell fate through epigenome reprogramming 72 samples shares modulates, fate
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.