GEO series

TGFβ inhibition during radiation therapy enhances immune cell infiltration and decreases metastases in a novel humanized mouse model Ewing sarcoma.

GSE261693 Homo sapiens (human) Single-cell RNA-seq 3 samples Submitted 2025/05/20 Platform GPL21697Platform GPL18573

At a glance

Single-cell RNA-seq · human · 3 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)
Topic: Ewing sarcomaThis series is part of our curated briefing on it.
Samples: 3 samples
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.

Summary (written by the submitters)

Ewing sarcoma is an aggressive cancer most commonly diagnosed in adolescents and young adults. Various mechanisms of TGFβ inhibition are being tested in clinical trials for patients with relapsed Ewing sarcoma. However, the functional impact of TGFβ inhibition on the Ewing tumor microenvironment remains largely unstudied given the historical lack of immunocompetent preclinical models of Ewing sarcoma.

Read the full summary ↓

Here, we use single cell RNAseq analysis of human Ewing tumors to demonstrate that immune cells are the largest source of TGFβ production in the human Ewing tumor microenvironment. We develop and utilize a humanized mouse model of Ewing sarcoma to study the effect of TGFβ inhibition on the Ewing tumor immune microenvironment both at baseline and during radiation therapy, a treatment that enhances TGFβ activation and is often used to treat patients with aggressive Ewing sarcoma. Finally, we utilize a bivalent ligand TGFβ TRAP and demonstrate that, in combination with radiation, TGFβ inhibition both increases immune cell infiltration in Ewing tumors and decreases lung metastatic burden.

This dataset

Open GSE261693 in finder → Find more human RNA-seq datasets → Ewing sarcoma 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 GSE261693_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 PRJNA1088440 and SRA study SRP495432. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Samples in this study

The sample list for this study is not cached yet. Press Load samples and it will be fetched from NCBI.

+ 3 more — browse all 3 samples with per-sample file links →

More Ewing sarcoma datasets

GSE299137 Autocrine TGFβ2 enforces a transcriptionally hybrid cell state in Ewing sarcoma 48 samples same disease briefing · shares tgf
GSE304126 CDK8 inhibition sequesters Med1 at EWS-FLI enhancers [RNA-Seq] 68 samples same disease briefing · shares inhibition
GSE338238 Menin inhibition impairs metastatic colonization of Ewing sarcoma 48 samples same disease briefing · shares inhibition
GSE332586 Mevalonate pathway activation in Ewing sarcoma reveals a 3D-specific synergy between statins and BCL-xL inhibition 36 samples same disease briefing · shares inhibition
GSE302426 CDK8 inhibition sequesters Med1 at EWS-FLI enhancers [ChIP-seq] 22 samples same disease briefing · shares inhibition
GSE302425 CDK8 inhibition sequesters Med1 at EWS-FLI enhancers [CUT&RUN] 12 samples same disease briefing · shares inhibition
GSE302424 CDK8 inhibition sequesters Med1 at EWS-FLI enhancers [ATAC-seq] 6 samples same disease briefing · shares inhibition
GSE260602 Cell context is the third axis of synergy for ATR inhibition and cisplatin in Ewing sarcoma 2 samples same disease briefing · shares inhibition

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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.