GEO series

Single nuclei transcriptomics from lumbar spinal cord of EAE mice treated with MIF nuclease inhibitor PAANIB1

GSE304067 Mus musculus (mouse) RNA-seq (gene expression) 17 samples Submitted 2025/10/24 Platform GPL34290

At a glance

RNA-seq (gene expression) · mouse · 17 samples

What it is: RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism: Mus musculus (mouse)
Samples: 17 samples: 6 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.
Paper: Autoimmune neuroinflammation leads to neuronal death via MIF nuclease-mediated parthanatosNature neuroscience · 2026

Summary (written by the submitters)

Central nervous system inflammation is implicated in neurodegeneration across several disorders, including multiple sclerosis (MS). While marked therapeutic progress has been made through the suppression of immune cell trafficking and function, primary neuroprotection in MS remains elusive. This, in part, is due to an incomplete understanding of the molecular signaling pathways involved in immune-mediated neuronal death.

Read the full summary ↓

Here, we show that parthanatos, a recently described caspase-independent and DNA damage-induced cell death program, contributes to neuron death in the experimental autoimmune encephalomyelitis (EAE) mouse model of autoimmune neuroinflammation. We revealed that DNA damage increases in neurons during EAE, and that neurons are progressively lost over the disease course. Neurons in affected areas display intercellular hallmarks of the parthanatos cascade. Genetic or pharmacologic blockade of the final step in parthanatos, genomic fragmentation by MIF nuclease, reduces neuron loss and disease severity. Transcriptomic characterization of these neurons reveals parthanatos-dependent differences in response to EAE. Together, this work establishes parthanatos as a key mechanism of neuron cell death during neuroinflammation.

Published in

Autoimmune neuroinflammation leads to neuronal death via MIF nuclease-mediated parthanatos

Mace JW, Gadani SP, Smith MD et al. · Nature neuroscience 2026 · PMID 41703302 · doi:10.1038/s41593-026-02201-7

This dataset

Open GSE304067 in finder → Find more mouse 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 GSE304067_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1298857 and SRA study SRP604754. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41703302) ↗

Study design

6 conditions, mostly in triplicate

EAE, PAANIB1, male, ×3 EAE, PAANIB1, female, ×3 EAE, Vehicle, male, ×3 EAE, Vehicle, female, ×3 CFA, PAANIB1, female, ×2 CFA, Vehicle, female, ×2 Unassigned Reads, ×1

Supports a between-group comparison across 16 samples.

How we read this: 6 replicated groups read from 17 sample titles; they account for 16 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

GSM9142608 CFA, PAANIB1, female, rep 1 CFA, PAANIB1, female,
GSM9142609 CFA, PAANIB1, female, rep 2 CFA, PAANIB1, female,
GSM9142610 CFA, Vehicle, female, rep 1 CFA, Vehicle, female,
GSM9142611 CFA, Vehicle, female, rep 2 CFA, Vehicle, female,
GSM9142612 EAE, PAANIB1, male, rep 1 EAE, PAANIB1, male,
GSM9142613 EAE, PAANIB1, male, rep 2 EAE, PAANIB1, male,
GSM9142614 EAE, PAANIB1, male, rep 3 EAE, PAANIB1, male,
GSM9142615 EAE, PAANIB1, female, rep 1 EAE, PAANIB1, female,
GSM9142616 EAE, PAANIB1, female, rep 3 EAE, PAANIB1, female,
GSM9142617 EAE, PAANIB1, female, rep 2 EAE, PAANIB1, female,
GSM9142618 EAE, Vehicle, male, rep 1 EAE, Vehicle, male,
GSM9142619 EAE, Vehicle, male, rep 2 EAE, Vehicle, male,
GSM9142620 EAE, Vehicle, male, rep 3 EAE, Vehicle, male,
GSM9142621 EAE, Vehicle, female, rep 3 EAE, Vehicle, female,
GSM9142622 EAE, Vehicle, female, rep 1 EAE, Vehicle, female,
GSM9142623 EAE, Vehicle, female, rep 2 EAE, Vehicle, female,
GSM9142624 Unassigned Reads, rep 1

Datasets on a similar topic

GSE304068 MIF Nuclease Inhibition Protects CNS Neurons following Inflammation. 27 samples shares mif, nuclease
GSE281907 Spinal cord bulk RNA sequencing of an EAE mouse model of multiple sclerosis 16 samples shares eae, spinal
GSE281176 Spinal cord single-nuclei RNA sequencing of an EAE mouse model of multiple sclerosis 16 samples shares eae, spinal
GSE287324 Transcriptomic analysis of spinal cord in day 35 experimental autoimmune encephalomyelitis (EAE) model 10 samples shares eae, spinal
GSE298720 Global gene expression profiles were compared among IL1B-treated, Ad-OSCAR-treated, and control mice, with or without subsequent treatment with OSCAR inhibitors (Brivudine or Adefovir). 35 samples shares inhibitor, treated
GSE201128 The response to lipopolysaccharide (LPS) of bone marrow derived macrophages treated with oxysterol binding protein (OSBP) inhibitors 30 samples shares inhibitor, treated
GSE266241 Reduction of inhibitory signaling and selective induction of C-C motif chemokine ligands after spinal cord ischemia 29 samples shares inhibitor, spinal
GSE282271 Global transcriptional profiles of mouse intestinal organoids treated with IFN-g or/and MEK inhibitor [RNA-Seq] 26 samples shares inhibitor, treated

Search all mouse RNA-seq 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.