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Molecular indicators of hepatocellular carcinoma resistance to Y-90 microspheres revealed through high-throughput screening of cell lines and transcriptomics

GSE312144 Homo sapiens (human) RNA-seq (gene expression) 51 samples Submitted 2025/12/12 Platform GPL34284
At a glance

RNA-seq (gene expression) · human · 51 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
51 samples: 17 conditions, mostly in triplicateGroups 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
Epithelial-Mesenchymal Transition and Stress Adaptations Underlie Yttrium-90 Resistance in Liver Cancer Cell LinesCancer research communications · 2026
Summary (written by the submitters)
Molecular signatures predict prognosis in hepatocellular carcinoma; however, their relevance to Y-90 radioembolization remains unknown. Here, we perform Y-90 microsphere screens in a panel of genetically diverse human HCC cell lines. Ten transcriptomically diverse human HCC cell lines were exposed to 20 MBq of Y-90 glass beads. Normalized AUC values qualified sensitivity.
Read the full summary ↓
Whole-transcriptome RNA sequencing at baseline and post-treatment underwent differential expression analysis and gene set enrichment analysis. The response of HCC cell lines to Y-90 was heterogeneous, with SK-Hep1 and SNU-449 being the most resistant and PLC/PRF/5 being the most sensitive.
Published in
Epithelial-Mesenchymal Transition and Stress Adaptations Underlie Yttrium-90 Resistance in Liver Cancer Cell Lines
Zheleznyak A, Duraiyan D, Thunuguntla P et al. · Cancer research communications 2026 · PMID 41411069 · doi:10.1158/2767-9764.CRC-25-0627
This dataset
Open GSE312144 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 GSE312144_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 PRJNA1372480 and SRA study SRP650551. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41411069) ↗
Study design
17 conditions, mostly in triplicate
SNU-387_baseline ×3 Hep-G2_baseline ×3 SNU-423_baseline ×3 SNU-449_baseline ×3 SNU-475_baseline ×3 Hep-3B_baseline ×3 SK-Hep1_baseline ×3 SNU-398_baselime ×3 +9 more

Supports a case/control comparison: 21 samples read as cases, 27 as controls.

How we read this: 17 replicated groups read from 51 sample titles; they account for 51 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

+ 11 more — browse all 51 samples with per-sample file links →

More Hepatocellular carcinoma datasets

Search all human RNA-seq datasets in GEO →

Share this dataset

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.