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The contribution of Arpc5 for gene expression in intestinal macrophages

GSE298655 Mus musculus (mouse) RNA-seq (gene expression) 72 samples Submitted 2025/11/20 Platform GPL34328
At a glance

RNA-seq (gene expression) · mouse · 72 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
72 samples
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
Branched actin networks mediate macrophage-dependent host-microbiota homeostasisScience (New York, N.Y.) · 2025
Summary (written by the submitters)
Patients with loss-of-function mutations in the ARPC5 subunit of the Arp2/3 complex develop inflammation and immunodeficiency after birth, leading to early mortality. However, the mechanistic basis for these phenotypes remains obscure. Our work demonstrate that loss of Arpc5 in the murine hematopoietic system causes early-onset intestinal inflammation.
Read the full summary ↓
This condition is initiated by microbiota breaching the ileal mucosa, leading to local and systemic inflammation. Macrophage infiltrate into the ileum, but in the absence of Arpc5 fail to restrict microbial invasion. So, we wanted to investigate the Arpc5 contribution for intestinal macrophages expression.
Published in
Branched actin networks mediate macrophage-dependent host-microbiota homeostasis
Vasconcellos LRC, Huang SCM, Suarez-Bonnet A et al. · Science (New York, N.Y.) 2025 · PMID 41231985 · doi:10.1126/science.adr9571
This dataset
Open GSE298655 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 GSE298655_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 PRJNA1270842 and SRA study SRP589217. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41231985) ↗
Samples in this study

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