GEO series

Perturbed liver gene zonation in a mouse model of non-alcoholic steatohepatitis

GSE248077 Mus musculus (mouse) RNA-seq (gene expression) 13 samples Submitted 2024/08/01 Platform GPL24247

At a glance

RNA-seq (gene expression) · mouse · 13 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: 13 samples: 7 × NASH, vs 6 × Chow,Groups 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.

Summary (written by the submitters)

Liver zonation characterizes the separation of metabolic pathways along the lobules and is required for optimal hepatic function. Wnt signaling is a master regulator of spatial liver zonation. A perivenous-periportal Wnt activity gradient orchestrates metabolic zonation by activating genes in perivenous hepatocytes, while suppressing genes in their periportal counterparts.

Read the full summary ↓

The understanding of liver gene zonation and zonation regulators in disease was limited. Non-alcoholic steatohepatitis (NASH) is a chronic liver disease characterized by fat accumulation, inflammation, and fibrosis. Here, we investigated the perturbation of liver gene zonation in a mouse NASH model by combination of spatial transcriptomics, bulk RNAseq and in situ hybridization. Wnt target genes represented a major subset of genes showing altered spatial expression in the NASH liver. The altered Wnt target gene expression level and zonation spatial pattern were in line with the upregulation of Wnt regulators and the augmentation of Wnt signaling. Particularly, we found that the Wnt activator Rspo3 expression was restricted to the perivenous zone in control livers, whereas expanded to the periportal zone in NASH livers. AAV8-mediated RSPO3 overexpression in controls resulted in a zonation change, and further amplified the disturbed zonation of Wnt target genes in NASH, but had no impacts on steatosis, inflammation and fibrosis. In summary, our study demonstrated the alteration of Wnt signaling in a mouse NASH model, leading to perturbed liver zonation.

This dataset

Open GSE248077 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 GSE248077_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 PRJNA1041737 and SRA study SRP472524. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

7 × NASH, vs 6 × Chow,

Supports a between-group comparison across 13 samples.

How we read this: 2 replicated groups read from 13 sample titles; they account for 13 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

GSM7905572 Chow, Bio Rep 1 Chow,
GSM7905573 Chow, Bio Rep 2 Chow,
GSM7905574 Chow, Bio Rep 3 Chow,
GSM7905575 Chow, Bio Rep 4 Chow,
GSM7905576 Chow, Bio Rep 5 Chow,
GSM7905577 Chow, Bio Rep 6 Chow,
GSM7905578 NASH, Bio Rep 1 NASH,
GSM7905579 NASH, Bio Rep 2 NASH,
GSM7905580 NASH, Bio Rep 3 NASH,
GSM7905581 NASH, Bio Rep 4 NASH,
GSM7905582 NASH, Bio Rep 5 NASH,
GSM7905583 NASH, Bio Rep 6 NASH,
GSM7905584 NASH, Bio Rep 7 NASH,

Datasets on a similar topic

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GSE256505 Sex differences in Non-Alcoholic Steatohepatitis (NASH) in mice evoked by a fructose-palmitate-cholesterol (FPC)-enriched diet 49 samples shares steatohepatitis, non-alcoholic
GSE233051 A cyclic peptide-grafted Fc with hepatocyte growth factor functionality ameliorates hepatic fibrosis in a non-alcoholic steatohepatitis mouse model. 36 samples shares steatohepatitis, non-alcoholic
GSE279351 Liver-specific inactivation of Cideb improves metabolic profiles and ameliorates steatohepatitis and fibrosis in animal models for MASH 45 samples shares steatohepatitis, liver
GSE261088 Gene expression profile at single cell level of non-parenchymal cells from Fibrosis and Tumor (FAT) Metabolic Dysfunction-Associated Steatohepatitis (MASH) model vs healthy liver at 12- and 24-week timepoints. 4 samples shares steatohepatitis, liver
GSE206338 Deconvolution of cell types from bulk gene expression profiling in a nonalcoholic steatohepatitis model of mice liver reveals global alteration of macrophages and hepatic stellate cells 4 samples shares steatohepatitis, liver
GSE256377 Hepatic stellate cells control liver zonation and function via R-spondin 3 [bulkRNAseq_mouse_HSCdepleted] 34 samples shares zonation, liver
GSE67918 Non-alcoholic steatohepatitis causes selective CD4+ T cell loss and promotes hepatocarcinogenesis 12 samples shares steatohepatitis, non-alcoholic

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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.