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

GSE289109 Mus musculus (mouse) Single-nucleus RNA-seq 20 samples Submitted 2025/12/23 Platform GPL24247Platform GPL24676
At a glance

Single-nucleus RNA-seq · mouse · 20 samples

What it is
Single-nucleus RNA-seqGene activity measured in individual nuclei (used when whole cells are hard to isolate, for example from frozen tissue).
Organism
Mus musculus (mouse)
Samples
20 samples: 7 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 GSE289109 in finder → Find more RNA-seq 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 GSE289109_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1221549 and SRA study SRP562713. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41448185) ↗
Study design
7 conditions, mostly in duplicate
RasmussenEncephalitisHC_NeuNpos_Patient ×2 CNCHCNEG ×2 CNCHCPOS ×2 CC10HCNEG ×2 CC10HCPOS ×2 CC70HCNEG ×2 CC70HCPOS ×2 CC10HC ×1 +5 more

Supports a between-group comparison across 14 samples.

How we read this: 7 replicated groups read from 20 sample titles; they account for 14 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
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