GEO series

Intercellular communication between hepatic stellate cells and myofibroblasts mediated by osteopontin and FGF18

GSE285364 Mus musculus (mouse) Single-cell RNA-seq 3 samples Submitted 2025/05/24 Platform GPL24247

At a glance

Single-cell RNA-seq · mouse · 3 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: 3 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: Intercellular communication between hepatic stellate cells and myofibroblasts mediated by osteopontin and FGF18 promotes liver fibrosisiScience · 2025

Summary (written by the submitters)

Purpose: To further explore FGF18's role in liver fibrosis beyond its known effects on HSC proliferation and TGFβ signaling, we performed RNA sequencing on primary HSCs treated with FGF18 or TGF-b. Methods: Fresh isolated HSCs were starved with DMEM containing 0.2% FBS for 24 hours and then left untreated or stimulated with FGF18 (100 ng/mL), TGFb1 (1 ng/mL).

Read the full summary ↓

Total RNA was extracted from HSCs using RNeasy Micro Kit (74004, QIAGEN). RNA libraries were prepared using the SMART-Seq HT PLUS Kit (R400748, Takara Bio) according to the manufacturer's protocol.Paired-end sequencing (2 × 150 bp) was performed on a NovaSeq 6000 system (Illumina) to generate approximately 40M reads (20M pairs) per sample, with a target of 6G bases per sample. Results: RNA-seq analysis revealed that FGF18 induced Ccnd1 while suppressing profibrotic genes such as Col1a2, Col3a1, and Acta2, whereas TGFβ showed opposite effects. Among 62 genes upregulated by both factors, we focused on Spp1, encoding osteopontin, given its known role in tissue fibrosis.

Published in

Intercellular communication between hepatic stellate cells and myofibroblasts mediated by osteopontin and FGF18 promotes liver fibrosis

Seki T, Komazawa-Sakon S, Nishina T et al. · iScience 2025 · PMID 40678531 · doi:10.1016/j.isci.2025.112932

This dataset

Open GSE285364 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 GSE285364_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 PRJNA1203227 and SRA study SRP553908. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40678531) ↗

Samples in this study

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+ 3 more — browse all 3 samples with per-sample file links →

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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.