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Gene expression profiling of NAT10 knockdown in HepG2 hepatocellular carcinoma cells by QuantSeq 3' mRNA-seq

GSE336019 Homo sapiens (human) RNA-seq (gene expression) 8 samples Submitted 2026/06/25 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 8 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
8 samples: 4 × HepG2 siControl vs 4 × HepG2 siNAT10 knockdownGroups 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)
NAT10 (N-acetyltransferase 10) is an RNA acetyltransferase that catalyzes N4-acetylcytidine (ac4C) modification of mRNA and rRNA. To investigate the transcriptomic consequences of NAT10 depletion, we performed siRNA-mediated knockdown of NAT10 in HepG2 hepatocellular carcinoma cells. Total RNA was extracted using TRI reagent 2 days after siRNA transfection, and 3' mRNA-seq libraries were prepared using the Lexogen QuantSeq 3' mRNA-Seq Library Prep Kit FWD.
Read the full summary ↓
Sequencing was performed on Illumina NovaSeq 6000. Four biological replicates per condition were analyzed: samples 1, 2, 5, 6 are negative control siRNA (siCtrl), and samples 3, 4, 7, 8 are siNAT10 knockdown.
This dataset
Open GSE336019 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 GSE336019_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 PRJNA1480589 and SRA study SRP711346. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
4 × HepG2 siControl vs 4 × HepG2 siNAT10 knockdown

Supports a case/control comparison: 4 samples read as cases, 4 as controls.

How we read this: 2 replicated groups read from 8 sample titles; they account for 8 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.