GEO series

mRNA Sequencing Analysis of MCM7 Knockdown in Primary Hepatocytes Under IL-6 Stimulation

GSE276001 Mus musculus (mouse) RNA-seq (gene expression) 12 samples Submitted 2025/08/09 Platform GPL34290

At a glance

RNA-seq (gene expression) · mouse · 12 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: 12 samples: 3 × Primary hepatocyte,shControl vs 3 × Primary hepatocyte,shMCM7 vs 3 × Primary hepatocyte,shControl,IL6 sitimulated 24h vs 3 × Primary hepatocyte,shMCM7,,IL6 sitimulated 24hGroups 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: MCM7 promotes liver fibrosis by transcriptionally regulating IL11 via the SHCBP1-RACGAP1-STAT3 axisCell death & disease · 2025

Summary (written by the submitters)

Liver fibrosis, marked by excessive extracellular matrix deposition, remains a significant challenge due to its complex and not fully understood mechanisms. This study explores the role of Minichromosome Maintenance Complex Component 7 (MCM7) in the development of liver fibrosis, with a focus on its regulatory network and interactions.

Read the full summary ↓

We knocked down MCM7 in primary hepatocytes and exposed them to IL-6 to simulate inflammatory conditions. RNA sequencing was then utilized to identify the differentially expressed genes and pathways influenced by MCM7 depletion. The results revealed notable alterations in gene expression, particularly in fibrosis- and inflammation-related pathways. Our study identified MCM7 as a key regulator of IL11 expression through the SHCBP1-RACGAP1-STAT3 signaling pathway, which contributes to the activation of hepatic stellate cells and the advancement of liver fibrosis. These findings underscore the critical role of MCM7 in liver fibrosis by promoting IL11 expression, thereby driving the activation of hepatic stellate cells and the progression of fibrosis. Overall, this research sheds light on a mechanistic pathway where MCM7 plays a pivotal role in liver fibrosis progression through the regulation of IL11 expression under inflammatory conditions.

Published in

MCM7 promotes liver fibrosis by transcriptionally regulating IL11 via the SHCBP1-RACGAP1-STAT3 axis

Wang C, Ye M, Xu T et al. · Cell death & disease 2025 · PMID 40789837 · doi:10.1038/s41419-025-07937-x

This dataset

Open GSE276001 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 GSE276001_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 PRJNA1154255 and SRA study SRP529450. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40789837) ↗

Study design

3 × Primary hepatocyte,shControl vs 3 × Primary hepatocyte,shMCM7 vs 3 × Primary hepatocyte,shControl,IL6 sitimulated 24h vs 3 × Primary hepatocyte,shMCM7,,IL6 sitimulated 24h

Supports a between-group comparison across 12 samples.

How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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

GSM8489256 Primary hepatocyte,shControl 1 Primary hepatocyte,shCo…
GSM8489257 Primary hepatocyte,shControl 2 Primary hepatocyte,shCo…
GSM8489258 Primary hepatocyte,shControl 3 Primary hepatocyte,shCo…
GSM8489259 Primary hepatocyte,shMCM7 1 Primary hepatocyte,shMC…
GSM8489260 Primary hepatocyte,shMCM7 2 Primary hepatocyte,shMC…
GSM8489261 Primary hepatocyte,shMCM7 3 Primary hepatocyte,shMC…
GSM8489262 Primary hepatocyte,shControl,IL6 sitimulated 24h 1 Primary hepatocyte,shCo…
GSM8489263 Primary hepatocyte,shControl,IL6 sitimulated 24h 2 Primary hepatocyte,shCo…
GSM8489264 Primary hepatocyte,shControl,IL6 sitimulated 24h 3 Primary hepatocyte,shCo…
GSM8489265 Primary hepatocyte,shMCM7,,IL6 sitimulated 24h 1 Primary hepatocyte,shMC…
GSM8489266 Primary hepatocyte,shMCM7,,IL6 sitimulated 24h 2 Primary hepatocyte,shMC…
GSM8489267 Primary hepatocyte,shMCM7,,IL6 sitimulated 24h 3 Primary hepatocyte,shMC…

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