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Gene expression profile at single cell level of neuroblastoma tumors

GSE218450 Homo sapiens (human) Single-cell RNA-seq 16 samples Submitted 2024/05/01 Platform GPL18573
At a glance

Single-cell RNA-seq · human · 16 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism
Homo sapiens (human)
Topic
NeuroblastomaThis series is part of our curated briefing on it.
Samples
16 samples: 4 × M993AAA_T1_scR_CEL-Seq2 vs 3 × M609AAA_T1_scR_CEL-Seq2 vs 3 × M787AAA_T2_scR_CEL-Seq2 vs 2 × M017AAB_T1_scR_CEL-Seq2Groups 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
Effective methods for bulk RNA-seq deconvolution using scnRNA-seq transcriptomesGenome biology · 2023
Summary (written by the submitters)
Single cell expression data used for training the deconvolution algorithm
Published in
Effective methods for bulk RNA-seq deconvolution using scnRNA-seq transcriptomes
Cobos FA, Panah MJN, Epps J et al. · Genome biology 2023 · PMID 37528411 · doi:10.1186/s13059-023-03016-6
This dataset
Open GSE218450 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 GSE218450_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 PRJNA903879. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 37528411) ↗
Study design
4 × M993AAA_T1_scR_CEL-Seq2 vs 3 × M609AAA_T1_scR_CEL-Seq2 vs 3 × M787AAA_T2_scR_CEL-Seq2 vs 2 × M017AAB_T1_scR_CEL-Seq2

Supports a between-group comparison across 12 samples.

How we read this: 4 replicated groups read from 16 sample titles; they account for 12 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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