Single-cell analyses of metastatic bone marrow in human neuroblastoma reveals microenvironmental remodeling and metastatic signature
Single-cell RNA-seq · human · 15 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
- 15 samples: 6 × NBBM vs 3 × BMGroups 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 analyses of metastatic bone marrow in human neuroblastoma reveals microenvironmental remodeling and metastatic signatureJCI insight · 2024
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 GSE220946_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 PRJNA912132 and SRA study SRP524626. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 9 samples.
How we read this: 2 replicated groups read from 15 sample titles; they account for 9 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.
- GSM6830350 NBBM1 NBBM
- GSM6830351 NBBM2 NBBM
- GSM6830352 NBBM3 NBBM
- GSM6830354 NBBM4 NBBM
- GSM6830355 NBBM5 NBBM
- GSM6830356 NBBM6 NBBM
- GSM6830357 BM10 BM
- GSM6830358 BM6 BM
- GSM6830359 BM7 BM
- GSM6830360 NB21-BM2R
- GSM6830362 NB33-BM3
- GSM6830363 NB34_BM
- GSM6830364 NB35-BM1
- GSM6830365 NB37-BM5
- GSM6830366 NB34_Bone
- 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.