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Transcriptomic profiling of isolated hepatic macrophage subsets (Kupffer cells, Monocyte-derived Macrophages and Monocytes) in common bile duct ligated (CBDL)-mice, mice with acute colitis (DSS), and combinations (CBDL+DSS)

GSE183687 Mus musculus (mouse) RNA-seq (gene expression) 58 samples Submitted 2024/08/29 Platform GPL19057
At a glance

RNA-seq (gene expression) · mouse · 58 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
58 samples: 7 conditions, mostly with about 12 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
Osteopontin characterizes bile duct-associated macrophages and correlates with liver fibrosis severity in primary sclerosing cholangitisHepatology (Baltimore, Md.) · 2024
Summary (written by the submitters)
In this study, we aimed to unravel the transcriptional profiles of specific hepatic macrophage subsets during cholestatic liver injury, acute colitis and when colitis is induced as a second hit on advanced cholestatic liver injury. Differentially expressed genes (DEGs) and corresponding pathways were determined via DESeq2 in R and STRING-App comparing groups or cell types as outlined in the 'overall design' section below.
Read the full summary ↓
Our results highlight the heterogeneity of the liver macrophage (MF) pool and describe functional differences between MF subsets. Longitudinally, the CBDL-associated expression profiles of each macrophage subset remained mostly stable. CBDL-induced cholestatic liver injury was characterized by the emergence of Trem2/Spp1 expressing monocyte-derived macrophages (MoMFs). DSS-colitis as a second hit on cholestatic liver injury enhanced this phenotype of MoMFs.
Published in
Osteopontin characterizes bile duct-associated macrophages and correlates with liver fibrosis severity in primary sclerosing cholangitis
De Muynck K, Heyerick L, De Ponti FF et al. · Hepatology (Baltimore, Md.) 2024 · PMID 37535809 · doi:10.1097/HEP.0000000000000557
This dataset
Open GSE183687 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 GSE183687_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 PRJNA761692 and SRA study SRP336184. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 37535809) ↗
Study design
7 conditions, mostly with about 12 replicates each
CBDL6w ×12 CBDL2w ×12 DSS ×11 CBDL+DSS ×8 Sham6w ×6 CBDL+DSS_Rep4+ ×3 Sham6w_Rep1+2+ ×2 Sham6w_Rep3+ ×1 +3 more

Supports a between-group comparison across 54 samples.

How we read this: 7 replicated groups read from 58 sample titles; they account for 54 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

+ 18 more — browse all 58 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

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