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Sequential adaptive changes in a c-Myc-driven model of hepatocellular carcinoma

GSE303515 Mus musculus (mouse) RNA-seq (gene expression) 34 samples Submitted 2025/07/28 Platform GPL19057
At a glance

RNA-seq (gene expression) · mouse · 34 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
34 samples: 7 conditions, mostly with about 5 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
Reversible dissociation of mitochondrial Complex V balances anabolic and energy-generating needs in canceriScience · 2026
Summary (written by the submitters)
Hepatocellular carcinoma (HCC) is a common cancer that frequently overexpresses the c-Myc (Myc) oncoprotein. Using a mouse model of Myc-induced HCC, we studied the metabolic, biochemical, and molecular changes accompanying HCC progression, regression, and recurrence. These involved altered rates of pyruvate and fatty acid β-oxidation and the likely re-directing of glutamine into biosynthetic rather than energy-generating pathways.
Read the full summary ↓
Initial tumors also showed reduced mitochondrial mass and differential contributions of electron transport chain complexes I and II to respiration. The uncoupling of complex II's electron transport function from its succinate dehydrogenase activity also suggested a mechanism by which Myc generates reactive oxygen species. RNA sequence studies revealed an orderly progression of transcriptional changes involving pathways pertinent to DNA damage repair, cell cycle progression, insulin-like growth factor signaling, innate immunity, and further metabolic re-programming. Only a subset of functions deregulated in initial tumors was similarly deregulated in recurrent tumors thereby indicating that the latter can “normalize” some behaviors to suit their needs. An interactive and freely available software tool was developed to allow continued analyses of these and other transcriptional profiles. Collectively, these studies define the metabolic, biochemical, and molecular events accompanyingHCCevolution, regression, and recurrence in the absence of any potentially confounding therapies.
Published in
Reversible dissociation of mitochondrial Complex V balances anabolic and energy-generating needs in cancer
Wang H, Lu J, Henchy C et al. · iScience 2026 · PMID 41732272 · doi:10.1016/j.isci.2026.114889
This dataset
Open GSE303515 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 GSE303515_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 PRJNA1295551 and SRA study SRP603069. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41732272) ↗
Study design
7 conditions, mostly with about 5 replicates each
Control Liver, ×5 Liver, Day 3 post-Myc induction, ×5 Liver, Day 7 post-Myc induction, ×5 Regressing liver tumor, Day 3 post-Myc suppre… ×5 Regressing liver tumor, Day 7 post-Myc suppre… ×5 Recurrent liver tumor, post-Myc reactivation … ×5 Liver tumor, Day 21–28 post-Myc induction, ×4

Supports a case/control comparison: 19 samples read as cases, 5 as controls.

How we read this: 7 replicated groups read from 34 sample titles; they account for 34 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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