Transcriptional programs dictating tumor cell fate decisions in neuroblastoma lymph node metastasis [bulk RNA-seq]
Single-cell RNA-seq · human · 18 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
- 18 samples: 18 samples, each with a distinct title — no replicated groupsGroups 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 and Spatial Omics Reveals Region-Specific Plasticity and Therapeutic Vulnerabilities in Metastatic High-Risk NeuroblastomabioRxiv : the preprint server for biology · 2025
Read the full summary ↓
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 GSE309267_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 PRJNA1334992 and SRA study SRP627891. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 18 sample titles: 18 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.
- GSM9264111 UPN1443P_RNA-seq
- GSM9264112 UPN2538P_RNA-seq
- GSM9264113 UPN2099P_RNA-seq
- GSM9264114 UPN2424P_RNA-seq
- GSM9264115 UPN3651P_RNA-seq
- GSM9264116 UPN3729P_RNA-seq
- GSM9264117 UPN3765P_RNA-seq
- GSM9264118 UPN3709P_RNA-seq
- GSM9264119 UPN3728P_RNA-seq
- GSM9264120 UPN3770P_RNA-seq
- GSM9264121 UPN1443M_RNA-seq
- GSM9264122 UPN200M_RNA-seq
- GSM9264123 UPN2113M_RNA-seq
- GSM9264124 UPN3031M_RNA-seq
- GSM9264125 UPN3284M_RNA-seq
- GSM9264126 UPN1177M_RNA-seq
- GSM9264127 UPN2099M_RNA-seq
- GSM9264128 UPN536M_RNA-seq
- GSE289930 Proteogenomic Characterization of Primary Oral Cancer Unveils Extracellular Matrix Remodeling and Immunosuppressive Microenvironment Linked to Lymph Node Metastasis [RNA-seq] 33 samples shares metastasis, rna-seq, lymph
- GSE253785 Bone morphogenetic protein (BMP) signaling determines neuroblastoma cell fate and sensitivity to retinoic acid [RNA-seq] 17 samples shares neuroblastoma, rna-seq, fate
- GSE49711 RNA-Seq reveals an unprecedented complexity of the neuroblastoma transcriptome and is suitable for clinical endpoint prediction [RNA-Seq] 498 samples shares neuroblastoma, rna-seq
- GSE308020 Integrative multi-omics deciphers the potential mechanism and microbial biomarkers for lymph node metastasis in colorectal cancer 66 samples shares metastasis, lymph
- GSE287496 CDK12 as an entry point for combination therapy in high-risk neuroblastoma [RNA-seq] 59 samples shares neuroblastoma, rna-seq
- GSE348445 Identification and Characterization of Adrenergic and Mesenchymal Cancer Cell States in Neuroblastoma Using Spatial-Omics [RNA-Seq] 33 samples shares neuroblastoma, rna-seq
- GSE253036 Tumor Cell JAGGED-1 Promotes Lymph Node Metastasis and Predicts Recurrence in Lymph Node Positive Breast Cancer Patients 27 samples shares metastasis, lymph
- GSE292598 YAPTAZ and neuroblastoma cell plasticity [RNA-Seq] 25 samples shares neuroblastoma, rna-seq
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.