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Spatially-restricted and ontogenically-distinct hepatic macrophages are required for tissue repair.

GSE280652 Mus musculus (mouse) Single-cell RNA-seq 42 samples Submitted 2024/10/30 Platform GPL24247Platform GPL21103
At a glance

Single-cell RNA-seq · mouse · 42 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism
Mus musculus (mouse)
Samples
42 samples: 36 distinct titles, 2 of them repeatedGroups 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
Spatially restricted and ontogenically distinct hepatic macrophages are required for tissue repairImmunity · 2025
Summary (written by the submitters)
Analysis of single cell RNA-seq, CITE-seq data and bulk RNA-seq data on cells isolated from the livers of mice following PBS and APAP (paracetamol/acetaminophen) administration. Spatial Transcriptomics analysis was performed using 10x Visium platform on mouse livers 48hrs post PBS or APAP administration. We also analysed single cell RNA-seq data on CD64+F4/80+ macrophages isolated from the livers of Trem2 fl/fl mice and CD64CRE Trem2 fl/fl mice.
Published in
Spatially restricted and ontogenically distinct hepatic macrophages are required for tissue repair
De Ponti FF, Bujko A, Liu Z et al. · Immunity 2025 · PMID 39862865 · doi:10.1016/j.immuni.2025.01.002
This dataset
Open GSE280652 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 GSE280652_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 PRJNA1179888 and SRA study SRP542061. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39862865) ↗
Study design
36 distinct titles, 2 of them repeated
CD64+F4/80+ macrophages from Trem2 fl/fl mice ×4 CD64+F4/80+ macrophages from CD64CRE Trem2 fl… ×4

How we read this: Read from 42 sample titles: 36 distinct titles with little repetition. 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

+ 2 more — browse all 42 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

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