GEO series

RIPK3 promotes neuronal survival by suppressing excitatory neurotransmission during CNS viral infection

GSE264436 Mus musculus (mouse) RNA-seq (gene expression) 18 samples Submitted 2025/02/03 Platform GPL21103

At a glance

RNA-seq (gene expression) · mouse · 18 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: 18 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: The kinase RIPK3 promotes neuronal survival by suppressing excitatory neurotransmission during central nervous system viral infectionImmunity · 2025

Summary (written by the submitters)

While recent work has identified roles for cytokines and inflammation in the regulation of neural activity, the capacity for cell intrinsic innate immune signaling within neurons to influence neurotransmission remains poorly understood. However, the existing evidence linking immune signaling with neuronal activity suggests that modulation of neurotransmission may serve previously undefined roles in host protection and pathogen control within the central nervous system.

Read the full summary ↓

Here, we identify a specialized function for RIPK3, a kinase traditionally associated with necroptotic cell death, in preserving neuronal survival during neurotropic flavivirus infection through the suppression of excitatory neurotransmission. We show that RIPK3 coordinates transcriptomic changes in neurons that suppress neuronal glutamate signaling, thereby desensitizing neurons to excitotoxic cell death. These effects occur independently of the traditional functions of RIPK3 in promoting MLKL-dependent necroptosis and NFκB-mediated inflammatory transcription. Instead, RIPK3 promotes phosphorylation of the key neural regulatory kinase CAMKII, which in turn activates the transcription factor CREB to drive a neuroprotective transcriptional program and suppress deleterious glutamatergic signaling. These findings identify an unexpected function for a canonical cell death protein in promoting neuronal survival during viral infection through the modulation of neuronal activity, highlighting new mechanisms of neuroimmune crosstalk.

Published in

The kinase RIPK3 promotes neuronal survival by suppressing excitatory neurotransmission during central nervous system viral infection

Estevez I, Buckley BD, Lindman M et al. · Immunity 2025 · PMID 39999836 · doi:10.1016/j.immuni.2025.01.017

This dataset

Open GSE264436 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 GSE264436_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 PRJNA1102407 and SRA study SRP502921. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39999836) ↗

Study design

6 conditions, mostly in triplicate

Neuron, control, ×3 Neuron, BB, ×3 Neuron, CREB inh, ×3 Neuron, CaMKII inh, ×3 Neuron, BB, CREB inh, ×3 Neuron, BB, CaMKII inh, ×3

Supports a between-group comparison across 18 samples.

How we read this: 6 replicated groups read from 18 sample titles; they account for 18 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

GSM8217974 Neuron, control, replicate 1 Neuron, control,
GSM8217975 Neuron, control, replicate 2 Neuron, control,
GSM8217976 Neuron, control, replicate 3 Neuron, control,
GSM8217977 Neuron, BB, replicate 1 Neuron, BB,
GSM8217978 Neuron, BB, replicate 2 Neuron, BB,
GSM8217979 Neuron, BB, replicate 3 Neuron, BB,
GSM8217980 Neuron, CREB inh, replicate 1 Neuron, CREB inh,
GSM8217981 Neuron, CREB inh, replicate 2 Neuron, CREB inh,
GSM8217982 Neuron, CREB inh, replicate 3 Neuron, CREB inh,
GSM8217983 Neuron, CaMKII inh, replicate 1 Neuron, CaMKII inh,
GSM8217984 Neuron, CaMKII inh, replicate 2 Neuron, CaMKII inh,
GSM8217985 Neuron, CaMKII inh, replicate 3 Neuron, CaMKII inh,
GSM8217986 Neuron, BB, CREB inh, replicate 1 Neuron, BB, CREB inh,
GSM8217987 Neuron, BB, CREB inh, replicate 2 Neuron, BB, CREB inh,
GSM8217988 Neuron, BB, CREB inh, replicate 3 Neuron, BB, CREB inh,
GSM8217989 Neuron, BB, CaMKII inh, replicate 1 Neuron, BB, CaMKII inh,
GSM8217990 Neuron, BB, CaMKII inh, replicate 2 Neuron, BB, CaMKII inh,
GSM8217991 Neuron, BB, CaMKII inh, replicate 3 Neuron, BB, CaMKII inh,

Datasets on a similar topic

GSE244086 MMPs and NETs are detrimental in CNS-tuberculosis with MMP inhibitor doxycycline improving murine CNS-tuberculosis survival (mouse) 69 samples shares cns, survival
GSE251784 ECM29/Proteasome-Mediated Self-Antigen Generation by CNS-Resident Neuroglia Promotes Regulatory T Cell Activation 47 samples shares cns, promotes
GSE288348 Disease-associated astrocyte epigenetic memory promotes CNS pathology [sgEp300, sgACLY astrocytes bulk RNA-Seq dataset] 18 samples shares cns, promotes
GSE301448 Epigenetic Reactivation of CNS Endothelial Developmental Programs Triggers Adult Brain Angiogenesis, Promotes Post-Stroke Revascularization and Neuroregeneration [RNAseq-Stroke] 18 samples shares cns, promotes
GSE280505 Leukaemia cell intrinsic and extrinsic factors cooperate to facilitate the survival and proliferation of KMT2A-rearranged B-ALL in the CNS niche. 16 samples shares cns, survival
GSE237891 Neuronal DAMPs exacerbate neurodegeneration via astrocytic RIPK3 signaling 13 samples shares ripk3, neuronal
GSE301293 Epigenetic Reactivation of CNS Endothelial Developmental Programs Triggers Adult Brain Angiogenesis, Promotes Post-Stroke Revascularization and Neuroregeneration. 12 samples shares cns, promotes
GSE252551 Disease-associated astrocyte epigenetic memory promotes CNS pathology [ATAC-Seq and RNA-Seq] 32 samples shares cns, promotes

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.