GEO series

Mapping self-associating chromatin hubs identifies Id proteins as key determinants of exhausted T cell fate

GSE310322 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 37 samples Submitted 2026/04/20 Platform GPL24247

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 37 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: 37 samples: 8 conditions, mostly in triplicateGroups 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.

Summary (written by the submitters)

This study aims to define how Id2 and Id3 regulate exhausted CD8+ T cell fate. We found that Id2 deletion reduced the Tex-eff population, whereas Id3 ablation in CD4-Cre mice diminished Tpex cells, indicating subset-specific roles for Id2 and Id3. Mechanistically, E2A is a major target of Id2/3, and Runx3 interacts with E2A. Pulldown of Id2/3 recovered both E2A and Runx3, supporting an Id2/3?E2A?Runx3 regulatory complex.

Read the full summary ↓

To map the genomic occupancy of Id2 and Id3, we expressed 3×T7-tagged Id2 or Id3 in in vitro-primed CD45.2+ P14 cells, adoptively transferred these cells into CD45.1 recipient mice, and infected the recipients with LCMV Clone 13. On day 6 post-infection, Tex-eff and Tpex cells were isolated for T7 CUT&RUN to define Id2 binding in Tex-eff cells and Id3 binding in Tpex cells, with the empty T7 vector backbone used as a negative control.

This dataset

Open GSE310322 in finder → Find more mouse ChIP / ATAC / CUT&Tag datasets →

Download · which file do I need?

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.

1 · Just have a look

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.

Series matrix ↓

2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE310322_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓

3 · Start from the raw reads

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.

Raw reads on ENA ↗

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 PRJNA1365760 and SRA study SRP647844. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

8 conditions, mostly in triplicate

Id3 WT, Stem, ATAC, ×3 Id3 WT, Term, ATAC, ×3 Id3 KO, Stem, ATAC, ×3 Id3 KO, Term, ATAC, ×3 Id2 WT, Stem, ATAC, ×3 Id2 WT, Term, ATAC, ×3 Id2 KO, Stem, ATAC, ×3 Id2 KO, Term, ATAC, ×3 +13 more

Supports a between-group comparison across 24 samples.

How we read this: 8 replicated groups read from 37 sample titles; they account for 24 of them. 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.

Samples in this study

GSM9293977 Id3 WT, Stem, ATAC, rep1 Id3 WT, Stem, ATAC,
GSM9293978 Id3 WT, Stem, ATAC, rep2 Id3 WT, Stem, ATAC,
GSM9293979 Id3 WT, Stem, ATAC, rep3 Id3 WT, Stem, ATAC,
GSM9293980 Id3 WT, Term, ATAC, rep1 Id3 WT, Term, ATAC,
GSM9293981 Id3 WT, Term, ATAC, rep2 Id3 WT, Term, ATAC,
GSM9293982 Id3 WT, Term, ATAC, rep3 Id3 WT, Term, ATAC,
GSM9293983 Id3 KO, Stem, ATAC, rep1 Id3 KO, Stem, ATAC,
GSM9293984 Id3 KO, Stem, ATAC, rep2 Id3 KO, Stem, ATAC,
GSM9293985 Id3 KO, Stem, ATAC, rep3 Id3 KO, Stem, ATAC,
GSM9293986 Id3 KO, Term, ATAC, rep1 Id3 KO, Term, ATAC,
GSM9293987 Id3 KO, Term, ATAC, rep2 Id3 KO, Term, ATAC,
GSM9293988 Id3 KO, Term, ATAC, rep3 Id3 KO, Term, ATAC,
GSM9293989 Id2 WT, Stem, ATAC, rep1 Id2 WT, Stem, ATAC,
GSM9293990 Id2 WT, Stem, ATAC, rep2 Id2 WT, Stem, ATAC,
GSM9293991 Id2 WT, Stem, ATAC, rep3 Id2 WT, Stem, ATAC,
GSM9293992 Id2 WT, Term, ATAC, rep1 Id2 WT, Term, ATAC,
GSM9293993 Id2 WT, Term, ATAC, rep2 Id2 WT, Term, ATAC,
GSM9293994 Id2 WT, Term, ATAC, rep3 Id2 WT, Term, ATAC,
GSM9293995 Id2 KO, Stem, ATAC, rep1 Id2 KO, Stem, ATAC,
GSM9293996 Id2 KO, Stem, ATAC, rep2 Id2 KO, Stem, ATAC,
GSM9293997 Id2 KO, Stem, ATAC, rep3 Id2 KO, Stem, ATAC,
GSM9293998 Id2 KO, Term, ATAC, rep1 Id2 KO, Term, ATAC,
GSM9293999 Id2 KO, Term, ATAC, rep2 Id2 KO, Term, ATAC,
GSM9294000 Id2 KO, Term, ATAC, rep3 Id2 KO, Term, ATAC,
GSM9608232 E2A rep1, WT Term, Cut&Run
GSM9608233 E2A rep2, WT Term, Cut&Run
GSM9608234 E2A rep1, Id2KO Term, Cut&Run
GSM9608235 E2A rep2, Id2KO Term, Cut&Run
GSM9608236 Runx3 rep1, WT Term, Cut&Run
GSM9608237 Runx3 rep2, WT Term, Cut&Run
GSM9608238 Runx3 rep1, Id2KO Term, Cut&Run
GSM9608239 Runx3 rep2, Id2KO Term, Cut&Run
GSM9613816 Id2 oe rep1, Term, Cut&Run
GSM9613817 Id2 oe rep2, Term, Cut&Run
GSM9613818 Id3 oe rep1, Stem, Cut&Run
GSM9613819 Id3 oe rep2, Stem, Cut&Run
GSM9613820 IgG, Cut&Run

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