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Multi-omics analysis of neuroblastoma cells reveals a diversity of malignant transformations

GSE130612 Homo sapiens (human) DNA methylation 64 samples Submitted 2021/08/19 Platform GPL17303Platform GPL17301
At a glance

DNA methylation · human · 64 samples

What it is
DNA methylationChemical marks on DNA that help switch genes on or off.
Organism
Homo sapiens (human)
Topic
NeuroblastomaThis series is part of our curated briefing on it.
Samples
64 samples
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 (NB) is a pediatric cancer of the developing sympathetic nervous system that exhibits significant variation in the stage of differentiation and cell composition of tumours. Global loss of DNA methylation and genomic 5-hydroxymethylcytosine (5hmC) is a hallmark of human cancers. Here, we used our recently developed single base resolution approaches, hmTOP-seq and uTOP-seq, for construction of 5hmC maps and identification of large hypomethylated domains (PMDs) in different NB cell subpopulations.
Read the full summary ↓
The 5hmC profiles revealed distinct signatures characteristic of different cell lineages and stages of malignant transformation of NB cells in a conventional and oxygen depleted environment, which often occurs in tumours. The analysis of the cell type-specific PMD distribution highlighted differences in global genome organization among NB cells that were ascribed to the same lineage identity by transcriptome assays. Collectively, we demonstrated a high informativeness of the integrative epigenomic and transcriptomic research in relation to large scale genome structure in investigating the mechanisms that regulate cell identities and developmental stages of NB cells. Such multi-omics analysis, as compared to mutational studies, open new ways for identification of novel disease-associated features which bring prognostic and therapeutic value in treating this aggressive pediatric disease.
This dataset
Open GSE130612 in finder → Find more human methylation 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 GSE130612_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: Look for beta-value tables or raw IDAT files among the supplementary files.

Also filed as BioProject PRJNA540775 and SRA study SRP194522. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 34557494) ↗
Samples in this study

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