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Core clock genetic control in the mouse hepatic stellate cell (HSC) EMS404

GSE304664 Mus musculus (mouse) RNA-seq (gene expression) 12 samples Submitted 2026/08/05 Platform GPL28457
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 × EMS404 cells, transfected with Bmal1 siRNA and treated with TGFb vs 3 × EMS404 cells, transfected with Bmal1 siRNA and treated with vehicle vs 3 × EMS404 cells, transfected with scrambled siRNA and treated with TGFb vs 3 × EMS404 cells, transfected with scrambled siRNA and treated with vehicleGroups 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
The circadian clock controls hepatic stellate cell activation via a BMAL1/CK1ε/REV-ERBα/transgelin signaling pathwayProceedings of the National Academy of Sciences of the United States of America · 2026
Summary (written by the submitters)
The impact of REVERBalpha agonism and of CLOCK:BMAL1 blockade on HSC activation was studied in the presence or not of the profibrotic stimulus TGFb
Published in
The circadian clock controls hepatic stellate cell activation via a BMAL1/CK1ε/REV-ERBα/transgelin signaling pathway
Johanns M, Berthier A, Vandel J et al. · Proceedings of the National Academy of Sciences of the United States of America 2026 · PMID 42479835 · doi:10.1073/pnas.2611767123
This dataset
Open GSE304664 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 GSE304664_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 PRJNA1302263 and SRA study SRP606911. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42479835) ↗
Study design
3 × EMS404 cells, transfected with Bmal1 siRNA and treated with TGFb vs 3 × EMS404 cells, transfected with Bmal1 siRNA and treated with vehicle vs 3 × EMS404 cells, transfected with scrambled siRNA and treated with TGFb vs 3 × EMS404 cells, transfected with scrambled siRNA and treated with vehicle

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
Datasets on a similar topic

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