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Genetic variation in the activity of a TREM2-p53 signaling axis determines oxygeninduced lung injury

GSE274969 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 77 samples Submitted 2025/07/24 Platform GPL21103
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 77 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
77 samples: 30 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
Genetic variation in the activity of a TREM2-p53 signaling axis determines oxygen-induced lung injuryNature immunology · 2025
Summary (written by the submitters)
To investigate the role of Trem2 in neonatal hyperoxia induced lung injury, we exposed mice to 75% oxygen for 14 days. We then performed gene expression profiling in whole lung and bone marrow derived macrophages using RNA-seq. We studied gene regulation using ChIP-seq.
Published in
Genetic variation in the activity of a TREM2-p53 signaling axis determines oxygen-induced lung injury
Abe Y, Spann NJ, Tang W et al. · Nature immunology 2025 · PMID 40715658 · doi:10.1038/s41590-025-02217-4
This dataset
Open GSE274969 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 GSE274969_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 PRJNA1148661 and SRA study SRP526712. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40715658) ↗
Study design
30 conditions, mostly in duplicate
B6_Nx_Lung ×6 B6_Hprx_Lung ×6 DBA_Nx_Lung ×4 DBA_Hprx_Lung ×4 T2KO_Nx_Lung ×4 T2KO_Hprx_Lung ×4 B6_Nx_Lung_ChIP_Input ×3 B6_Nx_BMDM ×2 +22 more

Supports a between-group comparison across 77 samples.

How we read this: 30 replicated groups read from 77 sample titles; they account for 77 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

+ 37 more — browse all 77 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

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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.