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Single-cell MultiOmics and spatial transcriptomics demonstrate neuroblastoma developmental plasticity

GSE183729 Homo sapiens (human) Spatial transcriptomics 18 samples Submitted 2025/01/23 Platform GPL16791
At a glance

Spatial transcriptomics · human · 18 samples

What it is
Spatial transcriptomicsGene activity measured with its position in a tissue section.
Organism
Homo sapiens (human)
Topic
NeuroblastomaThis series is part of our curated briefing on it.
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; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Paper
Single-cell MultiOmics and spatial transcriptomics demonstrate neuroblastoma developmental plasticityDevelopmental cell · 2025
Summary (written by the submitters)
To understand the cross-lineage transition of neuroblastoma. We performed RNA sequencing for bulk tissue of tumor xenografts
Published in
Single-cell MultiOmics and spatial transcriptomics demonstrate neuroblastoma developmental plasticity
Xu Y, Lou D, Chen P et al. · Developmental cell 2025 · PMID 40347947 · doi:10.1016/j.devcel.2025.04.013
This dataset
Open GSE183729 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 GSE183729_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: Spatial studies usually ship Space Ranger style folders (count matrix plus tissue images). Look for them among the supplementary files.

Also filed as BioProject PRJNA761770 and SRA study SRP336242. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40347947) ↗
Study design
6 conditions, mostly in triplicate
SKNAS_Control P9225 ×3 SKNAS_Hmx1 P9225 ×3 LAN-1_Control P9225 ×3 LAN-1_Hmx1 P9225 ×3 KELLY_Control P9225 ×3 KELLY_Hmx1 P9225 ×3

Supports a between-group comparison across 18 samples.

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

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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.