GEO series

ARID1B loss drives sorafenib resistance through transcriptional reprogramming in hepatocellular carcinoma

GSE335769 Homo sapiens (human) RNA-seq (gene expression) 12 samples Submitted 2026/06/19 Platform GPL30882

At a glance

RNA-seq (gene expression) · human · 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: Homo sapiens (human)
Topic: Hepatocellular carcinomaThis series is part of our curated briefing on it.
Samples: 12 samples: 3 × HepG2 WT RNA-seq, DMSO, vs 3 × HepG2 WT RNA-seq, Sorafenib, vs 3 × HepG2 ARID1B-KO RNA-seq, DMSO, vs 3 × HepG2 ARID1B-KO RNA-seq, Sorafenib,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)

mRNA-seq was performed in HepG2 hepatocellular carcinoma cells to characterize transcriptional changes driven by ARID1B loss under sorafenib treatment. Wild-type (WT) and ARID1B-knockout (ARID1B-KO) HepG2 cells were treated with sorafenib (5 µM, 48 h) or DMSO vehicle, with three biological replicates per condition. DESeq2 interaction model identified ARID1B-dependent transcriptional responses to sorafenib. Preprint: https://doi.org/10.64898/2026.06.11.731725

This dataset

Open GSE335769 in finder → Find more human RNA-seq datasets → Hepatocellular carcinoma landscape →

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 GSE335769_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 PRJNA1479416 and SRA study SRP710415. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

3 × HepG2 WT RNA-seq, DMSO, vs 3 × HepG2 WT RNA-seq, Sorafenib, vs 3 × HepG2 ARID1B-KO RNA-seq, DMSO, vs 3 × HepG2 ARID1B-KO RNA-seq, Sorafenib,

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

GSM9820473 HepG2 WT RNA-seq, DMSO, rep1 HepG2 WT RNA-seq, DMSO,
GSM9820474 HepG2 WT RNA-seq, DMSO, rep2 HepG2 WT RNA-seq, DMSO,
GSM9820475 HepG2 WT RNA-seq, DMSO, rep3 HepG2 WT RNA-seq, DMSO,
GSM9820476 HepG2 WT RNA-seq, Sorafenib, rep1 HepG2 WT RNA-seq, Soraf…
GSM9820477 HepG2 WT RNA-seq, Sorafenib, rep2 HepG2 WT RNA-seq, Soraf…
GSM9820478 HepG2 WT RNA-seq, Sorafenib, rep3 HepG2 WT RNA-seq, Soraf…
GSM9820479 HepG2 ARID1B-KO RNA-seq, DMSO, rep1 HepG2 ARID1B-KO RNA-seq…
GSM9820480 HepG2 ARID1B-KO RNA-seq, DMSO, rep2 HepG2 ARID1B-KO RNA-seq…
GSM9820481 HepG2 ARID1B-KO RNA-seq, DMSO, rep3 HepG2 ARID1B-KO RNA-seq…
GSM9820482 HepG2 ARID1B-KO RNA-seq, Sorafenib, rep1 HepG2 ARID1B-KO RNA-seq…
GSM9820483 HepG2 ARID1B-KO RNA-seq, Sorafenib, rep2 HepG2 ARID1B-KO RNA-seq…
GSM9820484 HepG2 ARID1B-KO RNA-seq, Sorafenib, rep3 HepG2 ARID1B-KO RNA-seq…

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GSE140228 Landscape and Dynamics of Single Immune Cells in Hepatocellular Carcinoma 41 samples same disease briefing · shares hepatocellular
GSE14520 Gene expression data of human hepatocellular carcinoma (HCC) 488 samples same disease briefing · shares hepatocellular
GSE10143 Gene Expression in Fixed Tissues and Outcome in Hepatocellular Carcinoma 387 samples same disease briefing · shares hepatocellular
GSE107170 Molecular Signature of Hepatitis D Virus-Associated Hepatocellular Carcinoma 307 samples same disease briefing · shares hepatocellular
GSE10186 Integrative Transcriptome Analysis Reveals Common Molecular Subtypes of Human Hepatocellular Carcinoma 118 samples same disease briefing · shares hepatocellular
GSE114564 Identification of novel serum biomarkers in early-stage HCC patients. 118 samples same disease briefing

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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.