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A Mouse Model for Metabolic Dysfunction-associated Steatotic Liver Disease and Hepatocellular Carcinoma [RNA-seq]

GSE246221 Mus musculus (mouse) RNA-seq (gene expression) 148 samples Submitted 2024/06/17 Platform GPL24676Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 148 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
148 samples: 33 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
Summary (written by the submitters)
The lack of an appropriate preclinical model of metabolic dysfunction-associated steatotic liver disease (MASLD) that recapitulates the whole disease spectrum impedes exploration of disease pathophysiology and the development of effective treatment strategies.
Read the full summary ↓
Considering the fact that MASLD patients accompanying type 2 diabetes mellitus (T2DM) have high risk of developing metabolic dysfunction-associated steatohepatitis (MASH), advanced fibrosis, and HCC, we treated low-dose streptozotocin (STZ; 40 mg/kg) for 5 consecutive days and subsequently fed a high-fat diet (HFD) to male C57BL/6J mice at 7 weeks of age (STZ+HFD). STZ+HFD mice gradually developed fatty liver, MASH, hepatic fibrosis, and hepatocellular carcinoma (HCC) in the context of metabolic dysfunction. In particular, from 20 weeks of age, MASH was evident, and from 32 weeks of age, advanced fibrosis was developed. At 38 weeks, a proportion of STZ+HFD mice developed HCC, which was subsequently observed in all mice up to 68 weeks of age. Furthermore, the hepatic transcriptomic features of STZ+HFD mice closely reflected those of obese patients with T2DM, MASH and MASLD-related HCC. Notably, dietary changes and tirzepatide administration alleviated MASH, hepatic fibrosis, and hepatic tumorigenesis in STZ+HFD mice. In conclusion, a murine model recapitulating the main histopathologic, transcriptomic, and metabolic alterations observed in MASLD patients with metabolic dysfunction was successfully established.
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 GSE246221 in finder → Find more 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 GSE246221_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 PRJNA1032104 and SRA study SRP468408. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39090079) ↗
Study design
33 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 +25 more

Supports a case/control comparison: 58 samples read as cases, 17 as controls.

How we read this: 33 replicated groups read from 148 sample titles; they account for 148 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

+ 108 more — browse all 148 samples with per-sample file links →

Datasets on a similar topic

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