GEO series

Tissue-specific inflammation induced by constitutively active STING is mediated by enhanced TNF signaling

GSE244062 Mus musculus (mouse) RNA-seq (gene expression) 16 samples Submitted 2024/04/16 Platform GPL24247

At a glance

RNA-seq (gene expression) · mouse · 16 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: 16 samples: 4 × WT CTRL vs 4 × SAVI vs 4 × Tnfr1/2 KO vs 4 × SAVI Tnfr 1/2 KOGroups 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: Tissue inflammation induced by constitutively active STING is mediated by enhanced TNF signalingeLife · 2025

Summary (written by the submitters)

Constitutive activation of STING by gain-of-function mutations triggers manifestation of the systemic autoinflammatory disease STING-associated vasculopathy with onset in infancy (SAVI) in humans and in mice. Murine SAVI is characterized by T cell lymphopenia, severe inflammatory interstitial lung disease, neuroinflammation and neurodegeneration with only limited contribution of type I interferon signaling.

Read the full summary ↓

Here, we show that pharmacologic inhibition of TNF signaling in SAVI mice improved T cell lymphopenia, but had no effect on interstitial lung disease. However, complete blocking of TNF receptor signaling by knocking out TNFR1 and TNFR2 in SAVI mice rescued both, loss of thymocytes as well as interstitial lung disease. Furthermore, chronic STING signaling in lung endothelial cells of diseased mice enhanced transcription of cytokines, chemokines and adhesions proteins resulting in increased transendothelial migration of neutrophils across the endothelial barrier that could be reverted by genetic inactivation of TNFR1 and 2. Thus, our results demonstrate a pivotal role of TNFR-signaling in the development of SAVI-associated lung disease and suggest this pathway as promising target to ameliorate human SAVI

Published in

Tissue inflammation induced by constitutively active STING is mediated by enhanced TNF signaling

Luksch H, Schulze F, Geißler-Lösch D et al. · eLife 2025 · PMID 40111902 · doi:10.7554/eLife.101350

This dataset

Open GSE244062 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 GSE244062_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 PRJNA1021178 and SRA study SRP463322. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40111902) ↗

Study design

4 × WT CTRL vs 4 × SAVI vs 4 × Tnfr1/2 KO vs 4 × SAVI Tnfr 1/2 KO

Supports a between-group comparison across 16 samples.

How we read this: 4 replicated groups read from 16 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

GSM7805963 WT CTRL 1 WT CTRL
GSM7805964 WT CTRL 2 WT CTRL
GSM7805965 WT CTRL 3 WT CTRL
GSM7805966 WT CTRL 4 WT CTRL
GSM7805967 SAVI 1 SAVI
GSM7805968 SAVI 2 SAVI
GSM7805969 SAVI 3 SAVI
GSM7805970 SAVI 4 SAVI
GSM7805971 Tnfr1/2 KO 1 Tnfr1/2 KO
GSM7805972 Tnfr1/2 KO 2 Tnfr1/2 KO
GSM7805973 Tnfr1/2 KO 3 Tnfr1/2 KO
GSM7805974 Tnfr1/2 KO 4 Tnfr1/2 KO
GSM7805975 SAVI Tnfr 1/2 KO 1 SAVI Tnfr 1/2 KO
GSM7805976 SAVI Tnfr 1/2 KO 2 SAVI Tnfr 1/2 KO
GSM7805977 SAVI Tnfr 1/2 KO 3 SAVI Tnfr 1/2 KO
GSM7805978 SAVI Tnfr 1/2 KO 4 SAVI Tnfr 1/2 KO

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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.