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Neurons undergo IFNγ-driven persistent epigenetic shifts and synaptic remodeling in the inflamed brain [ChIP-Seq]

GSE289108 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 57 samples Submitted 2025/12/23 Platform GPL24247
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 57 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
57 samples: 21 conditions, mostly in duplicateGroups 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
Neurons undergo IFNγ-driven persistent epigenetic shifts and synaptopathy in encephalitisNeuron · 2026
Summary (written by the submitters)
Our study provides novel evidence that neuronal intrinsic epigenetic changes are established as a consequence of cytotoxic T cell-mediated immune attacks and persist long after the resolution of the inflammatory process and associate to long lasting synaptic loss
Published in
Neurons undergo IFNγ-driven persistent epigenetic shifts and synaptopathy in encephalitis
Shammas G, Piccinno M, Egervari K et al. · Neuron 2026 · PMID 41448185 · doi:10.1016/j.neuron.2025.11.006
This dataset
Open GSE289108 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 GSE289108_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 PRJNA1221548 and SRA study SRP562712. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41448185) ↗
Study design
21 conditions, mostly in duplicate
WT_CC10_H3K27ac_HC ×2 WT_CC10_H3K27me3_HC ×2 WT_CC10_H3K4me3_HC ×2 WT_CC30_H3K27ac_HC ×2 WT_CC30_H3K27me3_HC ×2 WT_CC30_H3K4me3_HC ×2 WT_CC70_H3K27ac_HC ×2 WT_CC70_H3K27me3_HC ×2 +28 more

Supports a between-group comparison across 42 samples.

How we read this: 21 replicated groups read from 57 sample titles; they account for 42 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

+ 17 more — browse all 57 samples with per-sample file links →

Datasets on a similar topic

Search all mouse ChIP / ATAC / CUT&Tag datasets in GEO →

Share this dataset

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.