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The contribution of foam cells to angiogenesis and inflammation after spinal cord injury

GSE279731 Mus musculus (mouse) RNA-seq (gene expression) 48 samples Submitted 2024/11/01 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 48 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
48 samples: 12 conditions, mostly with about 4 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
Lipid accumulation in foam cells drives C1q-dependent synaptic loss and impairs motor function recovery after spinal cord injuryCommunications biology · 2025
Summary (written by the submitters)
After spinal cord injury (SCI), macrophages engage in the phagocytosis of myelin debris and dead cells, transforming into foam cells. Nevertheless, the ultimate fate and functional role of these foam cells remain unclear, while their inflammatory phenotype elicits ongoing controversy. We discovered that macrophages transform into foam cells through 3 stages, which were phagocytosis, digestion, and lipid overload.
Read the full summary ↓
Macrophages possess a certain degree of antioxidant capacity. When confronted with excessive lipid pressure, they undergo lipid droplets formation and metabolic reprogramming to alleviate lipotoxicity, also promoting angiogenesis. The anti-inflammatory phenotype of macrophages gradually diminished after SCI, phagocytosing debris could assist in maintaining this phenotype. Moreover, most genes expression patterns were conserved both in the SCI mice and rats. Our study provides a detailed description of the changes in gene expression and function during foam cell formation and long-term fate after SCI, which provides a theoretical basis for further research.
Published in
Lipid accumulation in foam cells drives C1q-dependent synaptic loss and impairs motor function recovery after spinal cord injury
Peng Y, Mulat Y, Yang Z et al. · Communications biology 2025 · PMID 41390852 · doi:10.1038/s42003-025-09167-5
This dataset
Open GSE279731 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 GSE279731_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 PRJNA1174164 and SRA study SRP539172. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41390852) ↗
Study design
12 conditions, mostly with about 4 replicates each
BMDM Control ×4 BMDM M1 ×4 BMDM M1_MD ×4 BMDM M2 ×4 BMDM M2_MD ×4 BMDM Baf ×4 BMDM Baze ×4 BMDM MD24 ×4 +4 more

Supports a between-group comparison across 48 samples.

How we read this: 12 replicated groups read from 48 sample titles; they account for 48 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

+ 8 more — browse all 48 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.