GEO series

Lipid influx enforces liver regeneration through the recruitment of CD36+ macrophages (scRNA-Seq and RNA-Seq)

GSE263879 Mus musculus (mouse) Single-cell RNA-seq 10 samples Submitted 2026/01/22 Platform GPL24247

At a glance

Single-cell RNA-seq · mouse · 10 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: 10 samples: 10 samples, each with a distinct title — no replicated groupsGroups 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.

Summary (written by the submitters)

The liver possesses a remarkable regeneration capacity under a wide variety of injury conditions, like partial hepatectomy (PHx) and over-dose acetaminophen (APAP) treatment. Macrophages, multitask at the wound site by facilitating wound debridement and producing chemokines, metabolites and growth factors, and consequently determine the balance between ongoing damage and repair following tissue injury.

Read the full summary ↓

CD36, which is universally expressed in a wide variety of cells (i.e., macrophages, adipocytes, myocytes, enterocytes and hepatocytes), and serves as the predominant fatty acid uptake facilitator of the cells to uptake microenvironmentally enriched lipids in various settings. However, the role for macrophage CD36 in mediating lipid accumulation as well as the regeneration of liver post physiological or pathophysiological injury still remains largely unknown. Herein, by utilizing multiple seq-based methods, we found the transient lipid accumulation in injured livers post PHx or APAP treatment exerted fundamental impacts on hepatic immune remodeling and induced the recruitment of macrophages with high level of CD36 expression and excessive lipid accumulation which facilitate the regeneration of livers. CD36-mediated lipid influx in macrophages triggers the activation of IRE1a signaling pathways via intracellular ceramide accumulation to promote high levels of IL6 production to accelerate liver regeneration.

This dataset

Open GSE263879 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 GSE263879_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 PRJNA1099666 and SRA study SRP501499. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

10 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 10 sample titles: 10 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

GSM8200487 sham
GSM8200488 PHx
GSM8209164 Liver, chow diet, 7day, rep3
GSM8209165 Liver, HFD, 7day, rep3
GSM8209166 KC, rep3
GSM8209167 LY6C+ MDM, rep3
GSM8209168 CD36+ MDM, rep3
GSM8209169 MDM-Ern1KO_CD36+ MDM, rep3
GSM8209170 Liver, Vehicle, rep4
GSM8209171 Liver, SSO, rep4

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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.