← BioTransfer GEO Dataset Finder
GEO series

Transcriptional landscape of MYCN-driven liver tumors

GSE302338 Homo sapiens (human) RNA-seq (gene expression) 38 samples Submitted 2025/07/16 Platform GPL28457Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 38 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
38 samples: 17 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.
Summary (written by the submitters)
Hepatocellular carcinoma (HCC) is a leading cause of cancer-related death, often diagnosed at advanced stages and characterized by high recurrence rates. While chronic liver inflammation and metabolic dysfunction are recognized contributors to tumorigenesis, the molecular mechanisms linking early microenvironmental stress to malignant transformation remain poorly understood.
Read the full summary ↓
MYCN, a proto-oncogenic transcription factor, has emerged as a potential biomarker of cancer stemness, yet its functional role in hepatocarcinogenesis is unclear. Here, we elucidate the oncogenic role of MYCN and its dynamic regulation during metabolic liver tumorigenesis.Using a transposon system in mice and the human hepatocyte cell line Hc, we demonstrate that MYCN overexpression functionally promotes liver tumorigenesis and hepatocyte transformation. Transcriptomic profiling of MYCN-driven tumors revealed molecular features resembling human HCC subtypes enriched in stress-adaptive gene programs, highlighting MYCN's role in shaping tumor-promoting transcriptional landscapes.
This dataset
Open GSE302338 in finder → Find more 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 GSE302338_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 PRJNA1290112 and SRA study SRP600071. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
17 conditions, mostly in duplicate
MYCN_AKT_early_50d ×4 MYCN_AKT_T_50d ×4 Control_3d ×2 MYCN_3d ×2 AKT_3d ×2 MYCN_AKT_3d ×2 Control_14d ×2 MYCN_14d ×2 +9 more

Supports a between-group comparison across 38 samples.

How we read this: 17 replicated groups read from 38 sample titles; they account for 38 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 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.