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KANSL3 directs transcriptional programs essential for hepatic metabolism and differentiation [RNA-seq]

GSE277829 Mus musculus (mouse) Single-cell RNA-seq 53 samples Submitted 2025/09/23 Platform GPL24247
At a glance

Single-cell RNA-seq · mouse · 53 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
53 samples: 14 conditions, mostly in triplicateGroups 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
KANSL3 directs transcriptional programs essential for hepatic metabolism and differentiationLife science alliance · 2025
Summary (written by the submitters)
Understanding the molecular mechanisms governing liver homeostasis and disease progression is essential for advancing therapeutic strategies for chronic liver diseases and hepatocellular carcinoma, with emerging evidence highlighting the pivotal role of epigenetic regulation in these progressive types of diseases. Here, we show that hepatic deletion of the epigenetic regulator KANSL3 initiates a series of pathological changes leading to early-onset chronic liver disease.
Read the full summary ↓
The absence of KANSL3 leads to biliary hyperplasia and early hepatic fibrosis. We identify KANSL3 as a master regulator of core hepatocyte gene expression through its regulation of histone acetylation, which significantly alters transcriptional networks in the liver. Single-cell RNA sequencing (scRNA-seq) analysis of Kansl3 liver knockout (LKO) animals reveals a marked shift in liver cellular composition following Kansl3 depletion. We show that the hepatic epithelial cells of Kansl3 LKO mice and Kansl3-depleted ductal organoids exhibit impaired differentiation into mature hepatocytes, uncovering the importance of KANSL3 in hepatic cell fate decisions. Ultimately, chronic loss of KANSL3 induces significant changes in the liver microenvironment, promoting a premalignant state characterized by an immunosuppressive environment linked to hepatocellular carcinoma (HCC) progression. These results highlight KANSL3 as a crucial regulator of liver homeostasis and a promising target for drug discovery.
Published in
KANSL3 directs transcriptional programs essential for hepatic metabolism and differentiation
Wiese M, Pessoa Rodrigues C, Akbas ME et al. · Life science alliance 2025 · PMID 41044006 · doi:10.26508/lsa.202503238
This dataset
Open GSE277829 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 GSE277829_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 PRJNA1164291 and SRA study SRP534278. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41044006) ↗
Study design
14 conditions, mostly in triplicate
RNAseq, Liver, P21, WT, ×6 RNAseq, Liver, P21, KO, ×6 RNAseq, Organoid, day15, KO, ×4 RNAseq, Organoid, day3, KO, ×4 RNAseq, Organoid, day6, KO, ×4 RNAseq, Organoid, day8, KO, ×4 RNAseq, Organoid, day4, KO, ×3 RNAseq, Organoid, day15, WT, ×3 +8 more

Supports a between-group comparison across 51 samples.

How we read this: 14 replicated groups read from 53 sample titles; they account for 51 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

+ 13 more — browse all 53 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

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