Single cell RNA sequencing of Ewing sarcoma tumors demonstrate transcriptional heterogeneity and clonal evolution
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
- Ewing sarcomaThis series is part of our curated briefing on it.
- Samples
- 15 samples: 8 × Blood sample from vs 7 × Primary tumor sampleGroups 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 RNA Sequencing of Ewing Sarcoma Tumors Demonstrates Transcriptional Heterogeneity and Clonal EvolutionClinical cancer research : an official journal of the American Association for Cancer Research · 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 GSE277083_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 PRJNA1160347. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 15 samples.
How we read this: 2 replicated groups read from 15 sample titles; they account for 15 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.
- GSM8513858 Primary tumor sample 001 Primary tumor sample
- GSM8513859 Primary tumor sample 005 Primary tumor sample
- GSM8513860 Primary tumor sample 010 Primary tumor sample
- GSM8513861 Primary tumor sample 038 Primary tumor sample
- GSM8513862 Primary tumor sample 051 Primary tumor sample
- GSM8513863 Primary tumor sample 061 Primary tumor sample
- GSM8513864 Primary tumor sample 066 Primary tumor sample
- GSM8513865 Blood sample from 001 Blood sample from
- GSM8513866 Blood sample from 002 Blood sample from
- GSM8513867 Blood sample from 005 Blood sample from
- GSM8513868 Blood sample from 006 Blood sample from
- GSM8513869 Blood sample from 009 Blood sample from
- GSM8513870 Blood sample from 010 Blood sample from
- GSM8513871 Blood sample from 012 Blood sample from
- GSM8513872 Blood sample from 038 Blood sample from
- GSE299137 Autocrine TGFβ2 enforces a transcriptionally hybrid cell state in Ewing sarcoma 48 samples same disease briefing · shares sarcoma, ewing
- GSE299432 Transcriptional Rewiring of BET Inhibitor Treated Ewing Sarcoma Cells Augments their Dependency on Focal Adhesion Kinase 30 samples same disease briefing · shares sarcoma, ewing
- GSE311851 LSD1 Performs Demethylase-Independent and Context-Specific Roles in Ewing Sarcoma 114 samples same disease briefing · shares sarcoma, ewing
- GSE338238 Menin inhibition impairs metastatic colonization of Ewing sarcoma 48 samples same disease briefing · shares sarcoma, ewing
- GSE229906 Chimeric protein EWS::FLI1 drives cell proliferation in Ewing Sarcoma via aberrant expression of KCNN1/SK1 and dysregulation of calcium signaling 45 samples same disease briefing · shares sarcoma, ewing
- GSE322664 Trabectedin and low-dose irinotecan to target EWS::FLI1 in Ewing sarcoma: a phase 1/2 trial 41 samples same disease briefing · shares sarcoma, ewing
- GSE332586 Mevalonate pathway activation in Ewing sarcoma reveals a 3D-specific synergy between statins and BCL-xL inhibition 36 samples same disease briefing · shares sarcoma, ewing
- GSE267222 STAG2 loss in Ewing sarcoma alters enhancer-promoter contacts dependent and independent of EWS::FLI1 32 samples same disease briefing · shares sarcoma, ewing
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.