Single-cell landscape analysis reveals distinct regression trajectories and novel prognostic biomarkers in primary neuroblastoma
Single-cell RNA-seq · human · 22 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
- 22 samples: 18 × A vs 2 × FGroups 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.
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.
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.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE287352_RAW.tar (it can run to tens of gigabytes).
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.
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 PRJNA1212194 and SRA study SRP558154. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 20 samples.
How we read this: 2 replicated groups read from 22 sample titles; they account for 20 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.
- GSM8744791 A16 A
- GSM8744792 LYG1206-2
- GSM8744793 A22 A
- GSM8744794 A17 A
- GSM8744795 A21 A
- GSM8744796 A5 A
- GSM8744797 A24 A
- GSM8744798 A50 A
- GSM8744799 A8 A
- GSM8744800 A51 A
- GSM8744801 A53 A
- GSM8744802 A49 A
- GSM8744803 A52 A
- GSM8744804 A32 A
- GSM8744805 S1
- GSM8744806 A12 A
- GSM8744807 A48 A
- GSM8744808 A41 A
- GSM8744809 A44 A
- GSM8744810 A45 A
- GSM8744811 F1 F
- GSM8744812 F2 F
- GSE183729 Single-cell MultiOmics and spatial transcriptomics demonstrate neuroblastoma developmental plasticity 18 samples same disease briefing · shares neuroblastoma, single-cell
- GSE178937 RNA sequencing of neuroblastoma cells treated with selinexor or with XPO1 knockdown 12 samples same disease briefing · shares neuroblastoma
- GSE275538 Identification of EPLIN as a novel MYCN-independent target in neuroblastoma and medulloblastoma 1 samples same disease briefing · shares neuroblastoma
- GSE120572 A mechanistic classification of clinical phenotypes in neuroblastoma 394 samples same disease briefing · shares neuroblastoma
- GSE181582 IGF2BP1 induces neuroblastoma via a druggable feedforward loop with MYCN promoting 17q oncogene expression 264 samples same disease briefing · shares neuroblastoma
- GSE12494 SNP data from Neuroblastoma samples 262 samples same disease briefing · shares neuroblastoma
- GSE16476 Integrated bioinformatic and wet-lab approach to identify potential oncogenic networks in neuroblastoma 88 samples same disease briefing · shares neuroblastoma
- GSE164456 Histone lysine demethylase 4 family proteins maintain the transcriptional program and adrenergic cellular state of MYCN-amplified neuroblastoma 69 samples same disease briefing · shares neuroblastoma
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.