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Role of metabolism in sorafenib-resistance hepatocellular carcinoma cellular model.

GSE273892 Mus musculus (mouse) RNA-seq (gene expression) 16 samples Submitted 2025/06/01 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 16 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
16 samples: 4 × p53-/-; Myc Hepatoblasts, control, 48h, vs 4 × p53-/-; Myc Hepatoblasts, drug, 48h, vs 4 × p53-/-; Myc Hepatoblasts, control, 7days, vs 4 × p53-/-; Myc Hepatoblasts, drug, 7days,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.
Paper
D-lactate and glycerol as potential biomarkers of sorafenib activity in hepatocellular carcinomaSignal transduction and targeted therapy · 2025
Summary (written by the submitters)
Hepatocellular carcinoma (HCC) is the most prevalent type of liver cancer and the third leading cause of cancer-related deaths worldwide. Potentially curative treatment of HCC involves various possibilities based on the stage of the disease. For the advanced stage of this disease, sorafenib is one of the first-line treatment options. It is an oral tyrosine kinase inhibitor, targeting several signalling pathways involved in tumor growth and angiogenesis.However, its usage is limited because many patients develop resistance after a short period (six months) of treatment.
Read the full summary ↓
Hepatoblasts knock-out for p53, and overexpressing Myconcogene(p53-/-; Myc) are used to reproduce the genetic settings of HCCin vitroand are treated with sorafenib attwo different time points: short (48 hours) and long (7 days) exposure. Thecombination oftranscriptomic and metabolomicdata was utilizedto unravel the effect of this drug on cellular metabolism and mitochondrial function,with the final aim of increasing the effectiveness of sorafenibtreatment.
Published in
D-lactate and glycerol as potential biomarkers of sorafenib activity in hepatocellular carcinoma
Pedretti S, Palermo F, Braghin M et al. · Signal transduction and targeted therapy 2025 · PMID 40571693 · doi:10.1038/s41392-025-02282-z
This dataset
Open GSE273892 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 GSE273892_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 PRJNA1143558 and SRA study SRP523948. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40571693) ↗
Study design
4 × p53-/-; Myc Hepatoblasts, control, 48h, vs 4 × p53-/-; Myc Hepatoblasts, drug, 48h, vs 4 × p53-/-; Myc Hepatoblasts, control, 7days, vs 4 × p53-/-; Myc Hepatoblasts, drug, 7days,

Supports a between-group comparison across 16 samples.

How we read this: 4 replicated groups read from 16 sample titles; they account for 16 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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