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Single-cell and bulk RNA sequencing of mouse atherosclerosis disease stage course [TRAP-seq]

GSE254396 Mus musculus (mouse) Single-cell RNA-seq 71 samples Submitted 2025/07/18 Platform GPL21626
At a glance

Single-cell RNA-seq · mouse · 71 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism
Mus musculus (mouse)
Samples
71 samples: 12 conditions, mostly with about 6 replicates eachGroups 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
Single-cell to pre-clinical evaluation of Trem2, Folr2, and Slc7a7 as macrophage-associated biomarkers for atherosclerosisCardiovascular research · 2025
Summary (written by the submitters)
Atherosclerotic coronary artery disease (CAD) development encompasses changes in immune cell activation across different tissues, including vascular and metabolic tissues. However, the specific disease-associated transcriptional changes occurring within each of the tissue cell types remain incompletely characterized. Here, we combine an atherosclerosis mouse model with a mouse strain designed for translating ribosome affinity purification followed by RNA sequencing (TRAP-Seq).
Read the full summary ↓
The mice express a fusion protein of EGFP and ribosomal protein L10a (EGFP-L10a) under the control of the macrophage-specific Csf1r (Cfms) promoter. Using EGFP as an affinity tag, this enables the enrichment of macrophage-specific ribosome-associated RNA from whole tissue lysates. Here, we profile the macrophage-enriched RNA fraction from aorta, liver and adipose tissue.
Published in
Single-cell to pre-clinical evaluation of Trem2, Folr2, and Slc7a7 as macrophage-associated biomarkers for atherosclerosis
Örd T, Palani S, Giroud Gerbetant J et al. · Cardiovascular research 2025 · PMID 41206594 · doi:10.1093/cvr/cvaf210
This dataset
Open GSE254396 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 GSE254396_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1070306 and SRA study SRP486393. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41206594) ↗
Study design
12 conditions, mostly with about 6 replicates each
adipose, LDLR+/+ ApoB+/+, chow diet, trap, ×6 adipose, LDLR-/- ApoB100/100, chow diet, trap, ×6 adipose, LDLR-/- ApoB100/100, 1 month high-fa… ×6 adipose, LDLR-/- ApoB100/100, 3 month high-fa… ×6 aorta, LDLR+/+ ApoB+/+, chow diet, trap, ×6 aorta, LDLR-/- ApoB100/100, chow diet, trap, ×6 aorta, LDLR-/- ApoB100/100, 1 month high-fat … ×6 liver, LDLR+/+ ApoB+/+, chow diet, trap, ×6 +4 more

Supports a between-group comparison across 71 samples.

How we read this: 12 replicated groups read from 71 sample titles; they account for 71 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

+ 31 more — browse all 71 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

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