← BioTransfer GEO Dataset Finder
GEO series

A human neural crest model reveals the developmental impact of neuroblastoma-associated chromosomal aberrations

GSE219153 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 154 samples Submitted 2024/03/22 Platform GPL20301Platform GPL24676
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 154 samples

What it is
ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
Organism
Homo sapiens (human)
Topic
NeuroblastomaThis series is part of our curated briefing on it.
Samples
154 samples: 20 conditions, mostly with about 4 replicates eachGroups 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.
Paper
A human neural crest model reveals the developmental impact of neuroblastoma-associated chromosomal aberrationsNature communications · 2024
SuperSeries — this record groups several sub-series.
Summary (written by the submitters)
This SuperSeries is composed of the SubSeries listed below.
Published in
A human neural crest model reveals the developmental impact of neuroblastoma-associated chromosomal aberrations
Saldana-Guerrero IM, Montano-Gutierrez LF, Boswell K et al. · Nature communications 2024 · PMID 38702304 · doi:10.1038/s41467-024-47945-7
This dataset
Open GSE219153 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 GSE219153_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 peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.

Also filed as BioProject PRJNA907257 and SRA study SRP496942. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38702304) ↗
Study design
20 conditions, mostly with about 4 replicates each
GEX ×26 BC ×12 17q1qMYCN_D9 ×4 17q1q_D0 ×4 17q1q_D3 ×4 17q1q_D9 ×4 17q_D0 ×4 17q_D3 ×4 +64 more

Supports a between-group comparison across 102 samples.

How we read this: 20 replicated groups read from 154 sample titles; they account for 102 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

+ 114 more — browse all 154 samples with per-sample file links →

More Neuroblastoma datasets

Search all human 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.