GEO series

Transcriptomic and epigenetic profiling of adrenergic and mesenchymal neuroblastomas with cell state conversion [RNA-Seq]

GSE299173 Homo sapiens (human) RNA-seq (gene expression) Submitted 2025/06/06

At a glance

RNA-seq (gene expression) · human

What it is: RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism: Homo sapiens (human)
Topic: NeuroblastomaThis series is part of our curated briefing on it.
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 accounts for 15% cancer related deaths in children, largely due to the disease relapse after multimodal therapy. Understanding the mechanism by which cancer cells acquire therapy resistance is critical to develop therapies for eradicating all cancer cells. Neuroblastoma are composed of two major cell states, adrenergic (ADRN) and mesenchymal (MES), which are presumed to interconvert and contribute to therapy resistance.

Read the full summary ↓

To better understand the cell plasticity of neuroblastoma in chemoresistance, we repeatedly treated human and murine neuroblastoma models with indisulam, a molecular glue drug that selectively degrades RBM39, a splicing factor critical to neuroblastoma cell survival. until these tumors developed full resistance. We then generated transcriptomic data, ATAC-seq data, CUT&Tag for H3K27Ac from these tumors, and defined their cell state features. These datasets provided a comprehensive transcriptomic and epigenetic profiling on ADRN and MES neuroblastoma cells after they developed therapy resistance. Here, we provided a detailed description of these unique datasets to facilitate their reusing. We anticipate that these datasets are useful resources to understand the role of cell lineage switching in therapy resistance.

This dataset

Open GSE299173 in finder → Find more RNA-seq datasets → Neuroblastoma landscape →

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 (GSE299173_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 ↓

What the files usually look like: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

NCBI GEO page ↗

Samples in this study

The sample list for this study is not cached yet. Press Load samples and it will be fetched from NCBI.

More Neuroblastoma datasets

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GSE178937 RNA sequencing of neuroblastoma cells treated with selinexor or with XPO1 knockdown 12 samples same disease briefing
GSE275538 Identification of EPLIN as a novel MYCN-independent target in neuroblastoma and medulloblastoma 1 samples same disease briefing
GSE120572 A mechanistic classification of clinical phenotypes in neuroblastoma 394 samples same disease briefing
GSE181582 IGF2BP1 induces neuroblastoma via a druggable feedforward loop with MYCN promoting 17q oncogene expression 264 samples same disease briefing
GSE12494 SNP data from Neuroblastoma samples 262 samples same disease briefing
GSE16476 Integrated bioinformatic and wet-lab approach to identify potential oncogenic networks in neuroblastoma 88 samples same disease briefing

Search all RNA-seq datasets in GEO →

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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.