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Identification and Characterization of Adrenergic and Mesenchymal Cancer Cell States in Neuroblastoma Using Spatial-Omics [RNA-Seq]

GSE348445 Homo sapiens (human) Single-cell RNA-seq 33 samples Submitted 2026/09/23 Platform GPL24676
At a glance

Single-cell RNA-seq · human · 33 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism
Homo sapiens (human)
Samples
33 samples: 24 distinct titles, 4 of them repeatedGroups 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 a pediatric cancer arising from the developing sympathoadrenal lineage and cell lines derived from neuroblastoma patients have features of either adrenergic neurons (ADRN) or mesenchymal cells (MES). However, identification of MES neuroblastoma cells in patient tumors has been challenging and controversial. This may be due to inter- or intra-patient tumor heterogeneity or discrepancies between the established neuroblastoma cell lines and patient tumors.
Read the full summary ↓
To characterize the intra- and inter-patient cellular heterogeneity, we analyzed 54 neuroblastoma tumors, spanning a broad range of clinical, genetic, and histologic features. We combined single-cell/nucleus RNA-seq (sc/scRNA-seq), bulk RNA-seq, spatial transcriptomics, and spatial proteomics. We discovered that the tumor cells are in distinct cellular neighborhoods from the non-malignant immune and stromal cells, but we could not identify MES neuroblastoma cells using the established gene expression signatures developed from cell lines. However, using ADRN/MES gene expression signatures developed from early passage orthotopic patient-derived xenografts, we were able to identify MES neuroblastoma tumor cells. We validated our results using RNA-seq, RNA in situ hybridization, immunostaining, chromatin profiling, spatial transcriptomics, functional studies in organoids, and electron microscopy. MES neuroblastoma tumor cells were more likely to be found in high-risk, MYCN amplified post-treatment samples. Taken together, our results demonstrate that MES neuroblastoma tumor cells are present in patient tumors and may correlate with response to therapy and outcome.
This dataset
Open GSE348445 in finder → Find more human RNA-seq datasets →
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 GSE348445_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1533985 and SRA study SRP739526. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
24 distinct titles, 4 of them repeated
SJNBL030721_X ×7 SJNBL030824_X ×2 SJNBL031239_X ×2 SJNBL071352_X ×2

How we read this: Read from 33 sample titles: 24 distinct titles with little repetition. 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
Datasets on a similar topic

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