GEO series

5-hydroxymethylcytosine deposition mediates Polycomb Repressive Complex 2 function in MYCN-amplified neuroblastoma [nano-seal, 5hmC]

GSE294304 Homo sapiens (human) Other 18 samples Submitted 2026/05/12 Platform GPL24676

At a glance

human · 18 samples

Organism: Homo sapiens (human)
Samples: 18 samples: 6 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.

Summary (written by the submitters)

MYCN-amplification is a strong predictor of poor prognosis in neuroblastoma, an embryonal malignancy that accounts for 15% of pediatric cancer deaths. Here, we found that MYCN-amplified neuroblastoma tumors have increased 5-hydroxymethylcytosine (5-hmC) deposition on Polycomb Repressive Complex 2 (PRC2) target genes. 5-hmC and H3K27me3, a catalytic product of PRC2, directly co-localize at the nucleosomal level in MYCN-amplified neuroblastoma.

Read the full summary ↓

Genes with co-localization of 5-hmC/H3K27me3 are involved in development related pathways and are transcriptionally repressed in MYCN-amplified neuroblastoma. Chemical and genetic inhibition of 5-hmC deposition results in a loss of H3K27me3 deposition on protein-coding genes. Furthermore, 5-hmC deposition predisposes H3K27me3 marked genes to transcriptional activation upon PRC2 inhibition with tazemetostat. Low expression of genes marked by 5-hmC/H3K27me3 is associated with poor clinical outcome. Our results suggest that 5-hmC/H3K27me3 co-operate to repress mediators of development highlighting a novel link between DNA modifications and chromatin modifications with potential therapeutic implications in MYCN-amplified neuroblastoma.

This dataset

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Download · which file do I need?

Direct links to NCBI, 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.

All supplementary files ↗

3 · The original raw files

Whole study · RAW.tar

Everything the authors deposited as one archive (GSE294304_RAW.tar), including the raw array or instrument files. Can be large; the picker in step 2 takes just the samples you need.

Whole study · RAW.tar ↓

Also filed as BioProject PRJNA1248982. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42502404) ↗

Study design

6 conditions, mostly in triplicate

WN, tazemetostat, 5hmC, ×3 WN, DMSO, 5hmC, ×3 BE2, tazemetostat, 5hmC, ×3 BE2, DMSO, 5hmC, ×3 BE2, C&R for H3K27me3 followed by nano-seal, … ×2 WN, C&R for H3K27me3 followed by nano-seal, 5… ×2 BE2, C&R for H3K27me3 followed by nano-seal n… ×1 WN, C&R for H3K27me3 followed by nano-seal ne… ×1

Supports a between-group comparison across 16 samples.

How we read this: 6 replicated groups read from 18 sample titles; they account for 16 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

GSM8902130 BE2, C&R for H3K27me3 followed by nano-seal, 5hmC, rep1 BE2, C&R for H3K27me3 f…
GSM8902131 WN, C&R for H3K27me3 followed by nano-seal, 5hmC, rep1 WN, C&R for H3K27me3 fo…
GSM8902132 WN, tazemetostat, 5hmC, rep1 WN, tazemetostat, 5hmC,
GSM8902133 WN, tazemetostat, 5hmC, rep2 WN, tazemetostat, 5hmC,
GSM8902134 WN, tazemetostat, 5hmC, rep3 WN, tazemetostat, 5hmC,
GSM8902135 WN, DMSO, 5hmC, rep1 WN, DMSO, 5hmC,
GSM8902136 WN, DMSO, 5hmC, rep2 WN, DMSO, 5hmC,
GSM8902137 WN, DMSO, 5hmC, rep3 WN, DMSO, 5hmC,
GSM8902138 BE2, tazemetostat, 5hmC, rep1 BE2, tazemetostat, 5hmC,
GSM8902139 BE2, tazemetostat, 5hmC, rep2 BE2, tazemetostat, 5hmC,
GSM8902140 BE2, tazemetostat, 5hmC, rep3 BE2, tazemetostat, 5hmC,
GSM8902141 BE2, DMSO, 5hmC, rep1 BE2, DMSO, 5hmC,
GSM8902142 BE2, DMSO, 5hmC, rep2 BE2, DMSO, 5hmC,
GSM8902143 BE2, DMSO, 5hmC, rep3 BE2, DMSO, 5hmC,
GSM8902144 BE2, C&R for H3K27me3 followed by nano-seal, 5hmC, rep2 BE2, C&R for H3K27me3 f…
GSM8902145 BE2, C&R for H3K27me3 followed by nano-seal neg control, 5hmC, rep1
GSM8902146 WN, C&R for H3K27me3 followed by nano-seal, 5hmC, rep2 WN, C&R for H3K27me3 fo…
GSM8902147 WN, C&R for H3K27me3 followed by nano-seal neg control, 5hmC, rep1

Datasets on a similar topic

GSE294307 5-hydroxymethylcytosine deposition mediates Polycomb Repressive Complex 2 function in MYCN-amplified neuroblastoma [CUT&Run] 18 samples shares 5-hydroxymethylcytosine, mycn-amplified, neuroblastoma, deposition, repressive, mediates
GSE294308 5-hydroxymethylcytosine deposition mediates Polycomb Repressive Complex 2 function in MYCN-amplified neuroblastoma [RNA-seq] 14 samples shares 5-hydroxymethylcytosine, mycn-amplified, neuroblastoma, deposition, repressive, mediates
GSE164456 Histone lysine demethylase 4 family proteins maintain the transcriptional program and adrenergic cellular state of MYCN-amplified neuroblastoma 69 samples shares mycn-amplified, neuroblastoma
GSE211354 The SAGA complex maintains the oncogenic gene expression program in MYCN-amplified neuroblastoma [RNA-Seq] 54 samples shares mycn-amplified, neuroblastoma
GSE112914 Differential gene expression analysis of MYCN-amplified neuroblastoma cells after Doxycycline inducible shRNA knockdown of JMJD6 gene expression 44 samples shares mycn-amplified, neuroblastoma
GSE211953 The SAGA complex maintains the oncogenic gene expression program in MYCN-amplified neuroblastoma [ChIP-Seq] 35 samples shares mycn-amplified, neuroblastoma
GSE285823 ATR inhibition synergizes with alkylating PI polyamide targeting MYCN by suppressing DNA repair in MYCN-amplified neuroblastoma 16 samples shares mycn-amplified, neuroblastoma
GSE248150 Nitric oxide inhibits ten-eleven translocation DNA demethylase activity to regulate 5mC and 5hmC across the genome [RNA-seq] 12 samples shares 5hmc

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