GEO series

EWSR1/FLI1 Expression in Human Mesenchymal Stem Cells derived from Experimental Teratomas Leads to Ewing´s Sarcoma Tumorigenesis [RNA-seq]

GSE272957 Homo sapiens (human) RNA-seq (gene expression) 16 samples Submitted 2025/01/31 Platform GPL16791

At a glance

RNA-seq (gene expression) · human · 16 samples

What it is: RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism: Homo sapiens (human)
Topic: Ewing sarcomaThis series is part of our curated briefing on it.
Samples: 16 samples: 8 × A vs 8 × BGroups 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.

Summary (written by the submitters)

Ewing sarcoma is an aggressive bone and soft tissue neoplasm, unique to humans, characterised by EWSR1/ETS rearrangements and whose cellular origin remains unknown. We report that human embryonic stem cells expressing EWSR1/FLI1 can form experimental teratomas. Mesenchymal stem-like cells (hMSLCs) isolated from these teratomas lack tumourigenic capacity despite retaining low levels of EWSR1/FLI1 expression.

Read the full summary ↓

Subsequent transduction of hMSLCs with EWSR1/FLI1 results in the expression of endothelial and neural genes, the acquisition of an Ewing sarcoma transcriptional signature and the formation of tumours in the spine and in soft tissues. These lesions are frequently haemorrhagic and composed of small round cells expressing discriminating markers of Ewing sarcoma. In summary, EWSR1/FLI1 enforces an aberrant endothelial-neural hybrid transcriptome and endows in vivo transforming capacity when expressed in a highly undifferentiated mesenchymal stem cell. This new experimental approach provides a test bench to elucidate the biology of translocation-dependent prenatal tumours, ranging from leukaemia to a variety of sarcomas.

This dataset

Open GSE272957 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 GSE272957_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1139713 and SRA study SRP521923. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

8 × A vs 8 × B

Supports a between-group comparison across 16 samples.

How we read this: 2 replicated groups read from 16 sample titles; they account for 16 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.

Samples in this study

GSM8415585 A1 A
GSM8415586 B1 B
GSM8415587 A2 A
GSM8415588 B2 B
GSM8415589 A8 A
GSM8415590 B8 B
GSM8415591 A9 A
GSM8415592 B9 B
GSM8415593 A10 A
GSM8415594 B10 B
GSM8415595 A11 A
GSM8415596 B11 B
GSM8415597 A12 A
GSM8415598 B12 B
GSM8415599 A13 A
GSM8415600 B13 B

More Ewing sarcoma datasets

GSE211743 KDM6A and B-mediated transcriptional activation of EWSR1-FLI1 targets coordinates demethylase dependent and independent mechanisms in Ewing sarcoma 99 samples same disease briefing · shares ewsr1, fli1, sarcoma
GSE317136 EWSR1::FLI1 Suppresses Ribosome Biogenesis and Creates a Targetable Vulnerability in Ewing Sarcoma 66 samples same disease briefing · shares ewsr1, fli1, sarcoma
GSE272960 EWS-FLI1 Expression in Human Embryonic Mesenchymal Stem Cells Leads to Defective DNA Damage Repair and Ewing Sarcoma 24 samples same disease briefing · shares fli1, mesenchymal, sarcoma
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 fli1, sarcoma
GSE322664 Trabectedin and low-dose irinotecan to target EWS::FLI1 in Ewing sarcoma: a phase 1/2 trial 41 samples same disease briefing · shares fli1, sarcoma
GSE267222 STAG2 loss in Ewing sarcoma alters enhancer-promoter contacts dependent and independent of EWS::FLI1 32 samples same disease briefing · shares fli1, sarcoma
GSE314154 STAG2 loss amplifies EWS-FLI1-driven microsatellite enhancer activity promoting Ewing's sarcoma aggressiveness [RNA-Seq] 20 samples same disease briefing · shares fli1, sarcoma
GSE231453 RNA-Seq of Ewing sarcoma shA673-1c cells after knockdown of EWS::FLI1 12 samples same disease briefing · shares fli1, sarcoma

Search all human RNA-seq datasets in GEO →

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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.