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Transcriptomic profiles of Huh7 and HLF hepatocellular carcinoma cells under 2D and 3D culture conditions

GSE298810 Homo sapiens (human) RNA-seq (gene expression) 12 samples Submitted 2026/04/22 Platform GPL24676
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: 6 conditions, mostly in duplicateGroups 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
A new inject-embed 3D culture method enables the spheroid and aggregate formation from single or dual liver cancer cell typesCancer cell international · 2026
Summary (written by the submitters)
This study investigates transcriptomic changes in human hepatocellular carcinoma (HCC) cell lines (Huh7 and HLF) cultured under different microenvironmental conditions, including 2D monolayer, 3D Inject-Embed, and 3D Mix-Embed cultures. RNA-seq was performed on total RNA using Illumina NovaSeq 6000 with paired-end 150 bp reads. Raw sequencing reads were aligned to the Homo sapiens reference genome (GRCh38/hg38) using STAR, and gene-level quantification was performed using featureCounts.
Read the full summary ↓
The dataset includes raw FASTQ files and processed count and FPKM matrices for each sample. This resource provides insights into the impact of 3D culture on liver cancer gene expression.
Published in
A new inject-embed 3D culture method enables the spheroid and aggregate formation from single or dual liver cancer cell types
Zhang H, Xue S, Pan J et al. · Cancer cell international 2026 · PMID 41792756 · doi:10.1186/s12935-026-04250-1
This dataset
Open GSE298810 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 GSE298810_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 PRJNA1271336 and SRA study SRP589515. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41792756) ↗
Study design
6 conditions, mostly in duplicate
Huh7 cells cultured under 2D condition, ×2 HLF cells cultured under 2D condition, ×2 Huh7 cells cultured under Inject-Embed condit… ×2 HLF cells cultured under Inject-Embed conditi… ×2 Huh7 cells cultured under Mix-Embed condition, ×2 HLF cells cultured under Mix-Embed condition, ×2

Supports a between-group comparison across 12 samples.

How we read this: 6 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
More Hepatocellular carcinoma datasets

Search all human RNA-seq datasets in GEO →

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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.