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A Stat1 gain-of-function mutant disrupts normal Stat4 innate lymphocyte programs during viral infection [scMulti-omics-seq]

GSE284323 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 10 samples Submitted 2025/06/13 Platform GPL24247
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 10 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
10 samples: 2 × Multiome_scRNAseq_MCMV D1.5, liver, WT, biol vs 2 × Multiome_scRNAseq_MCMV D1.5, liver, Stat1-GOF, biol vs 2 × Multiome_scATACseq_MCMV D1.5, liver, WT, biol vs 2 × Multiome_scATACseq_MCMV D1.5, liver, Stat1-GOF, biolGroups 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
An activating Stat1 mutant disrupts normal STAT4 innate lymphocyte programs during viral infectionScience immunology · 2025
Summary (written by the submitters)
Interferonopathies drive autoimmunity but can also impair host responses to pathogens including viral infection. To better understand viral susceptibility of patients with STAT1 gain-of-function (GOF) mutations, we generated conditional-knockin mouse models to elucidate disease mechanisms and relevance of different immune subsets. Virally infected Stat1-GOF mice exhibited impaired early IFN-γ production from innate lymphocytes, and lethality due to excess prolonged multi-cytokine production.
Read the full summary ↓
The presence of the Stat1-GOF allele resulted in premature usage of interferon-stimulated gene factor 3 (ISGF3) over the normal Stat4/AP-1 dependent transcriptomic program in activated innate lymphocytes. Administration of anti-IFN-γantibodies in wild-type (WT) mice after infection phenocopied Stat1-GOF mice presenting exaggerated inflammation despite viral control. Conversely, early administration of exogenous IFN-γ to infected Stat1-GOF mice prevented lethality and exaggerated cytokine response.Although Stat1-GOF mutations facilitate IFN-γ-mediated autoimmunity, early IFN-γ response to viral infection via a normal Stat4 program was impaired, leading to overcompensated inflammatory responses in Stat1-GOF mice.
Published in
An activating Stat1 mutant disrupts normal STAT4 innate lymphocyte programs during viral infection
Philips RL, Liao YC, Lau CM et al. · Science immunology 2025 · PMID 40446018 · doi:10.1126/sciimmunol.ado5986
This dataset
Open GSE284323 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 GSE284323_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 PRJNA1198592 and SRA study SRP551563. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40446018) ↗
Study design
2 × Multiome_scRNAseq_MCMV D1.5, liver, WT, biol vs 2 × Multiome_scRNAseq_MCMV D1.5, liver, Stat1-GOF, biol vs 2 × Multiome_scATACseq_MCMV D1.5, liver, WT, biol vs 2 × Multiome_scATACseq_MCMV D1.5, liver, Stat1-GOF, biol

Supports a between-group comparison across 8 samples.

How we read this: 4 replicated groups read from 10 sample titles; they account for 8 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
Datasets on a similar topic

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