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Circadian transcriptional profile of tissues with and without neutrophil depletion

GSE198770 Mus musculus (mouse) RNA-seq (gene expression) 191 samples Submitted 2025/01/09 Platform GPL17021
At a glance

RNA-seq (gene expression) · mouse · 191 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
191 samples: 6 conditions, mostly with about 36 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
Matrix-producing neutrophils populate and shield the skinNature · 2025
Summary (written by the submitters)
We previously reported that neutrophils infiltrate most tissues in a circadian fashion, as they clear out from the circulation (Casanova‑Acebes et al., 2018). In our current study we hypothesized that neutrophils are relevant contributors to the matrix of barrier tissues and that then their elimination should leave a temporal footprint in the circadian pattern of expression of matrix-associated genes.
Read the full summary ↓
To answer this question, we generated a circadian transcriptional dataset from the bone marrow, lung, liver, intestine and skin in wild type and neutrophil-depleted animals. The anlysis of the circadian patern of matrix related genes obtained from this datasets indicates that their temporal expression patterns in the analysed tissues is disrupted following neutrophil depletion. This results directly implicate neutrophils in the circadian biology of the matrix organization in various tissues.
Published in
Matrix-producing neutrophils populate and shield the skin
Vicanolo T, Özcan A, Li JL et al. · Nature 2025 · PMID 40108463 · doi:10.1038/s41586-025-08741-5
This dataset
Open GSE198770 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 GSE198770_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 PRJNA816850 and SRA study SRP364352. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40108463) ↗
Study design
6 conditions, mostly with about 36 replicates each
IBBM ×36 LIVE ×36 LU ×36 SKCODT ×16 SKDT ×16 SKBMAL ×15 zt1_1a81_INT ×1 zt1_1a82_INT ×1 +34 more

Supports a between-group comparison across 155 samples.

How we read this: 6 replicated groups read from 191 sample titles; they account for 155 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

+ 151 more — browse all 191 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.