← BioTransfer GEO Dataset Finder
GEO series

Transcriptional analysis of murine biliary atresia identifies macrophage heterogeneity and subset-specific macrophage functions

GSE287345 Mus musculus (mouse) RNA-seq (gene expression) 30 samples Submitted 2025/01/22 Platform GPL19057
At a glance

RNA-seq (gene expression) · mouse · 30 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
30 samples: 8 conditions, mostly with about 4 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
Transcriptional analysis of murine biliary atresia identifies macrophage heterogeneity and subset-specific macrophage functionsFrontiers in immunology · 2025
Summary (written by the submitters)
Macrophages play an important role in disease progression of pediatric cholestatic liver disease, particularly biliary atresia (BA); however, the restorative versus pathogenic role for precise macrophage subsets remains poorly defined. We aimed to distinguish the transcriptional profiles and roles of defined macrophage subset(s) in murine BA.
Read the full summary ↓
Ly6c+ macrophages demonstrated the greatest increase in numbers and percent of total macrophages in murine BA versus saline controls whereas MHCII+ macrophages decreased. Transcriptional changes in murine BA MHCII+ macrophages included reduced expression of the Kupffer cell gene signature, lower expression of genes involved in homeostatic processes, and increased expression of genes involved in inflammatory processes. Ly6c+ macrophages in murine BA showed increased expression for Hif1a and other genes involved in the cellular response to hypoxia. Among all subsets, the number of Ly6c+ macrophages exhibited the strongest correlation with severity of histologic liver injury by Ishak score. Our data identify specific pathways upregulated in Ly6c vs MHCII+ macrophage subsets in murine BA. Transcriptional similarities between murine BA and human cholestatic macrophages may enable translation of future mechanistic studies to new macrophage subset-specific therapies.
Published in
Transcriptional analysis of murine biliary atresia identifies macrophage heterogeneity and subset-specific macrophage functions
Gromer KD, Chen SY, Gadhvi G et al. · Frontiers in immunology 2025 · PMID 39949768 · doi:10.3389/fimmu.2025.1506195
This dataset
Open GSE287345 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 GSE287345_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 PRJNA1212167 and SRA study SRP558131. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39949768) ↗
Study design
8 conditions, mostly with about 4 replicates each
BALB/c Murine Hepatic Macrophages Ly6c+MHCII+… ×4 BALB/c Murine Hepatic Macrophages Ly6c+MHCII-… ×4 BALB/c Murine Hepatic Macrophages Ly6c-MHCII+… ×4 BALB/c Murine Hepatic Macrophages Ly6c+MHCII+… ×4 BALB/c Murine Hepatic Macrophages Ly6c+MHCII-… ×4 BALB/c Murine Hepatic Macrophages Ly6c-MHCII+… ×4 BALB/c Murine Hepatic Macrophages Ly6c-MHCII-… ×3 BALB/c Murine Hepatic Macrophages Ly6c-MHCII-… ×3

Supports a between-group comparison across 30 samples.

How we read this: 8 replicated groups read from 30 sample titles; they account for 30 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
Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

Share this dataset

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.