EWS-FLI1 Expression in Human Embryonic Mesenchymal Stem Cells Leads to Defective DNA Damage Repair and Ewing Sarcoma
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 24 samples
- What it is
- ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
- Organism
- Homo sapiens (human)
- Topic
- Ewing sarcomaThis series is part of our curated briefing on it.
- Samples
- 24 samples: 8 × A vs 8 × B vs 2 × EWGroups 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
- EWS::FLI1 expression in human embryonic mesenchymal stem cells leads to transcriptional reprograming, defective DNA damage repair and Ewing sarcomaNature communications · 2025
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 GSE272960_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: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.
Also filed as BioProject PRJNA1139710 and SRA study SRP521923. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 18 samples.
How we read this: 3 replicated groups read from 24 sample titles; they account for 18 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.
- 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
- GSM8415601 EW1 EW
- GSM8415602 EW2 EW
- GSM8415603 FL_E
- GSM8415604 FL_S
- GSM8415605 IgG_E
- GSM8415606 IgG_S
- GSM8415607 Inp_E
- GSM8415608 Inp_S
- GSE272957 EWSR1/FLI1 Expression in Human Mesenchymal Stem Cells derived from Experimental Teratomas Leads to Ewing´s Sarcoma Tumorigenesis [RNA-seq] 16 samples same disease briefing · shares mesenchymal, sarcoma, leads
- GSE314154 STAG2 loss amplifies EWS-FLI1-driven microsatellite enhancer activity promoting Ewing's sarcoma aggressiveness [RNA-Seq] 20 samples same disease briefing · shares ews-fli1, sarcoma
- GSE263504 Identification of genes regulated by knockdown of EWS-FLI1 in Ewing sarcoma cells. 12 samples same disease briefing · shares ews-fli1, sarcoma
- GSE291136 Dynamic modelling of EWS::FLI1 fluctuations reveals molecular determinants of phenotypic tumor plasticity and prognosis in Ewing sarcoma 222 samples same disease briefing · shares sarcoma
- GSE263234 ARID1A IDR Targets EWS-FLI1 Condensates and Finetunes Productive Chromatin Remodeling 12 samples same disease briefing · shares ews-fli1
- GSE318194 The effects of expression of the EWS-FLI1 oncoprotein on alternative splicing 6 samples same disease briefing · shares ews-fli1
- GSE176339 The Ewing Sarcoma Cell Line Atlas (ESCLA) 306 samples same disease briefing · shares sarcoma
- GSE17679 Inflammatory gene profiling of Ewing sarcoma family of tumors 117 samples same disease briefing · shares sarcoma
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.