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A Mouse Model for Metabolic Dysfunction-associated Steatotic Liver Disease and Hepatocellular Carcinoma

GSE246223 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 160 samples Submitted 2024/06/16 Platform GPL24676Platform GPL24247Platform GPL21273
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 160 samples

What it is
ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
Organism
Mus musculus (mouse)
Topic
Hepatocellular carcinomaThis series is part of our curated briefing on it.
Samples
160 samples: 37 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
A male mouse model for metabolic dysfunction-associated steatotic liver disease and hepatocellular carcinomaNature communications · 2024
SuperSeries — this record groups several sub-series.
Summary (written by the submitters)
This SuperSeries is composed of the SubSeries listed below.
Published in
A male mouse model for metabolic dysfunction-associated steatotic liver disease and hepatocellular carcinoma
Jeong BK, Choi WI, Choi W et al. · Nature communications 2024 · PMID 39090079 · doi:10.1038/s41467-024-50660-y
This dataset
Open GSE246223 in finder → Find more RNA-seq datasets → Hepatocellular carcinoma landscape →
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 GSE246223_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: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.

Also filed as BioProject PRJNA1032073 and SRA study SRP468408. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39090079) ↗
Study design
37 conditions, mostly with about 4 replicates each
STZ+HFD model, 56w, biological replication ×6 STZ+HFD model, 56w, hepatic tumor ID ×6 NAFLD patient, NAFLD activity score 2-3, fibr… ×6 NAFLD patient, NAFLD activity score 5-6, fibr… ×6 NAFLD patient, NAFLD activity score 4-7, fibr… ×6 Healthy control,7w, biological replication ×5 STZ+HFD model, 14w, biological replication ×5 STZ+HFD model, 20w, biological replication ×5 +29 more

Supports a case/control comparison: 58 samples read as cases, 20 as controls.

How we read this: 37 replicated groups read from 160 sample titles; they account for 160 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

+ 120 more — browse all 160 samples with per-sample file links →

More Hepatocellular carcinoma datasets

Search all 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.