GEO series

DNMT3B promotes neuroblastoma growth and survival, and its inhibition demonstrates antitumor effects.

GSE281320 Homo sapiens (human) RNA-seq (gene expression) 6 samples Submitted 2026/09/01 Platform GPL24676

At a glance

RNA-seq (gene expression) · human · 6 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: NeuroblastomaThis series is part of our curated briefing on it.
Samples: 6 samples: 3 × siControl vs 3 × siDNMT3BGroups 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)

Neuroblastoma is one of the most common childhood tumors and the current 5-year overall survival rate for children diagnosed at an advanced stage is less than 50%. Since tumor suppressor genes are often silenced via hypermethylation of promoter regions in tumors, DNA methylation has emerged as an attracting target against cancers. Despite the therapeutic potential of DNA methylation against neuroblastoma, conventional inhibitors of DNA methyltransferases have been reported to exhibit inadequate therapeutic effects and intolerable toxicities.

Read the full summary ↓

Therefore, another approach through to neuroblastoma therapy via DNA demethylation is required to address the demand for clinical applications. Here, we demonstrate that the inhibition of DNA methyltransferase 3B (DNMT3B) exerts anti-tumor effects by upregulating apoptosis-related genes and downregulating tumor progression. We found that RNAi-mediated inhibition of DNMT3B induces widespread DNA demethylation, leading to increased expression of apoptosis-related genes such as tumor protein p53, retinoblastoma 1, and upregulating cellular functions associated with apoptosis. Tumor progression was weakened in DNMT3B knockdown neuroblastoma cells in vitro and in vivo whereas was promoted in DNMT3B overexpression neuroblastoma cell lines. In addition, a DNMT3B inhibitor nanaomycin A exhibits anti-tumor effects with apoptosis and DNA demethylation of tumor cells in a neuroblastoma cell line derived mouse xenograft model. In conclusion, our findings support a key role for DNMT3B in a novel therapeutic strategy for neuroblastoma.

This dataset

Open GSE281320 in finder → Find more human RNA-seq datasets → Neuroblastoma 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 GSE281320_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 PRJNA1183374 and SRA study SRP543876. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

3 × siControl vs 3 × siDNMT3B

Supports a between-group comparison across 6 samples.

How we read this: 2 replicated groups read from 6 sample titles; they account for 6 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

GSM8618725 siControl_1 siControl
GSM8618726 siControl_2 siControl
GSM8618727 siControl_3 siControl
GSM8618728 siDNMT3B_1 siDNMT3B
GSM8618729 siDNMT3B_2 siDNMT3B
GSM8618730 siDNMT3B_3 siDNMT3B

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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.