GEO series

Organ injury in systemic autoimmunity is mediated by stem-like CD8 T cells arising from tissue-draining lymph nodes

GSE318514 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 45 samples Submitted 2026/04/20 Platform GPL24247

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 45 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: 45 samples: 45 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: Organ injury in systemic autoimmunity is mediated by stem-like CD8(+) T cells arising from tissue-draining lymph nodesImmunity · 2026

Summary (written by the submitters)

Chronic antigen exposure in cancer and infection generates hypofunctional, stem-like CD8 T cells that replenish tissue effector cells for tumor or pathogen control. CD8 T cells infiltrate kidneys in systemic lupus erythematosus, but their origin, differentiation, and function remain incompletely understood.

Read the full summary ↓

We identified in lupus-prone mice TCF1⁺ stem-like CD8 T cells in renal-draining lymph nodes that underwent TCR-dependent, antigen-driven expansion with differentiation into cytotoxic kidney-infiltrating cells that promoted tissue injury contingent on CD4 T cell help and IL-21/IL-15 signaling. CD8 T cell differentiation was marked by persistent AP-1 activity and cytotoxic function despite immune checkpoint upregulation. We found a parallel program of CD8 T cell differentiation in kidneys of patients with lupus nephritis, reflecting shared pathogenesis. This T cell differentiation program is analogous to that in chronic infections and cancer, indicating conservation across states of chronic antigen stimulation; however, CD8 T cells in systemic autoimmunity retain effector function despite terminal differentiation.

Published in

Organ injury in systemic autoimmunity is mediated by stem-like CD8(+) T cells arising from tissue-draining lymph nodes

Al Souz J, Wei Y, Cui C et al. · Immunity 2026 · PMID 42013863 · doi:10.1016/j.immuni.2026.03.022

This dataset

Open GSE318514 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 GSE318514_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 PRJNA1419135 and SRA study SRP674846. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42013863) ↗

Study design

45 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 45 sample titles: 45 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.

Samples in this study

GSM9496905 Cite with TCR, mouse 1 CD8 T cells, GEX
GSM9496906 Cite with TCR, mouse 1 CD8 T cells, TCR
GSM9496907 Cite with TCR, mouse 1 CD8 T cells, HTO
GSM9496908 Cite with TCR, mouse 2, eGFP positive, CD8 T cells, GEX
GSM9496909 Cite with TCR, mouse 2, eGFP positive, CD8 T cells, TCR
GSM9496910 Cite with TCR, mouse 2, eGFP positive, CD8 T cells, HTO
GSM9496911 Cite with TCR, mouse 2, eGFP negative, CD8 T cells, GEX
GSM9496912 Cite with TCR, mouse 2, eGFP negative, CD8 T cells, TCR
GSM9496913 Cite with TCR, mouse 2, eGFP negative, CD8 T cells, HTO
GSM9496914 Cite with TCR, mouse 3, eGFP positive, CD8 T cells, GEX
GSM9496915 Cite with TCR, mouse 3, eGFP positive, CD8 T cells, TCR
GSM9496916 Cite with TCR, mouse 3, eGFP positive, CD8 T cells, HTO
GSM9496917 Cite with TCR, mouse 3, eGFP negative, CD8 T cells, GEX
GSM9496918 Cite with TCR, mouse 3, eGFP negative, CD8 T cells, TCR
GSM9496919 Cite with TCR, mouse 3, eGFP negative, CD8 T cells, HTO
GSM9496920 Cite with TCR, mouse 4, eGFP positive, CD8 T cells, GEX
GSM9496921 Cite with TCR, mouse 4, eGFP positive, CD8 T cells, TCR
GSM9496922 Cite with TCR, mouse 4, eGFP positive, CD8 T cells, HTO
GSM9496923 Cite with TCR, mouse 4, eGFP negative, CD8 T cells, GEX
GSM9496924 Cite with TCR, mouse 4, eGFP negative, CD8 T cells, TCR
GSM9496925 Cite with TCR, mouse 4, eGFP negative, CD8 T cells, HTO
GSM9496926 Cite with TCR, mouse 2, eGFP positive, CD4 T cells, GEX
GSM9496927 Cite with TCR, mouse 2, eGFP positive, CD4 T cells, TCR
GSM9496928 Cite with TCR, mouse 2, eGFP positive, CD4 T cells, HTO
GSM9496929 Cite with TCR, mouse 2, eGFP negative, CD4 T cells, GEX
GSM9496930 Cite with TCR, mouse 2, eGFP negative, CD4 T cells, TCR
GSM9496931 Cite with TCR, mouse 2, eGFP negative, CD4 T cells, HTO
GSM9496932 Cite with TCR, mouse 3, eGFP positive, CD4 T cells, GEX
GSM9496933 Cite with TCR, mouse 3, eGFP positive, CD4 T cells, TCR
GSM9496934 Cite with TCR, mouse 3, eGFP positive, CD4 T cells, HTO
GSM9496935 Cite with TCR, mouse 3, eGFP negative, CD4 T cells, GEX
GSM9496936 Cite with TCR, mouse 3, eGFP negative, CD4 T cells, TCR
GSM9496937 Cite with TCR, mouse 3, eGFP negative, CD4 T cells, HTO
GSM9496938 Cite with TCR, mouse 4, eGFP positive, CD4 T cells, GEX
GSM9496939 Cite with TCR, mouse 4, eGFP positive, CD4 T cells, TCR
GSM9496940 Cite with TCR, mouse 4, eGFP positive, CD4 T cells, HTO
GSM9496941 Cite with TCR, mouse 4, eGFP negative, CD4 T cells, GEX
GSM9496942 Cite with TCR, mouse 4, eGFP negative, CD4 T cells, TCR
GSM9496943 Cite with TCR, mouse 4, eGFP negative, CD4 T cells, HTO
GSM9496944 Multiome, kidney T cells, GEX

+ 5 more — browse all 45 samples with per-sample file links →

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GSE269676 3D genome of CD8+ T cells reveals IRF8-mediated exhaustion in cancer 18 samples shares cd8, mediated
GSE275974 SATB1 is a key regulator of quiescence in stem-like CD8+ T cells [RNA-seq] 10 samples shares cd8, stem-like
GSE299305 3D genome of CD8+ T cells reveals IRF8-mediated exhaustion in cancer [Hi-C] 4 samples shares cd8, mediated
GSE296763 Mitochondrial respiration is necessary for CD8 T cell proliferation and cell fate 99 samples shares cd8
GSE329774 Metabolically and epigenetically reprogrammed splenic TRNP1hiCD8+ T cells exacerbate liver fibrosis 93 samples shares cd8

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