The hegemonic EWSR1::ETS oncogene overrules core regulatory circuitry mechanisms in Ewing sarcoma.
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 39 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
- 39 samples: 10 conditions, mostly in duplicateGroups 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
- The hegemonic EWSR1::ETS oncoprotein overrules core regulatory circuitry principles in Ewing sarcomaNPJ precision oncology · 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 GSE293632_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 PRJNA1245388 and SRA study SRP576042. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 24 samples.
How we read this: 10 replicated groups read from 39 sample titles; they account for 24 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.
- GSM8887379 CHLA-10, WT , R1 CHLA-10, WT ,
- GSM8887380 CHLA-10, WT , R2 CHLA-10, WT ,
- GSM8887381 CHLA-10, WT , R3 CHLA-10, WT ,
- GSM8887382 CHLA-10, KD , R1 CHLA-10, KD ,
- GSM8887383 CHLA-10, KD , R2 CHLA-10, KD ,
- GSM8887384 CHLA-10, KD , R3 CHLA-10, KD ,
- GSM8887385 SK-N-MC, siCT, R1 SK-N-MC, siCT,
- GSM8887386 SK-N-MC, siCT, R2 SK-N-MC, siCT,
- GSM8887387 SK-N-MC, siEF1, R1 SK-N-MC, siEF1,
- GSM8887388 SK-N-MC, siEF1, R2 SK-N-MC, siEF1,
- GSM8887389 MHH, ES1, siCT, R1 MHH, ES1, siCT,
- GSM8887390 MHH, ES1, siCT, R2 MHH, ES1, siCT,
- GSM8887391 MHH, ES1, siEF1, R1 MHH, ES1, siEF1,
- GSM8887392 MHH, ES1, siEF1, R2 MHH, ES1, siEF1,
- GSM8887393 RD-ES, WT, R1 RD-ES, WT,
- GSM8887394 RD-ES, WT, R2 RD-ES, WT,
- GSM8887395 RD-ES, WT, R3 RD-ES, WT,
- GSM8887396 RD-ES, KD, R1 RD-ES, KD,
- GSM8887397 RD-ES, KD, R2 RD-ES, KD,
- GSM8887398 RD-ES, KD, R3 RD-ES, KD,
- GSM8887399 TC-71, siCT, R1 TC-71, siCT,
- GSM8887400 TC-71, siCT, R2 TC-71, siCT,
- GSM8887401 TC-71, siEF1, R1 TC-71, siEF1,
- GSM8887402 TC-71, siEF1, R2 TC-71, siEF1,
- GSM8887403 EW-1 cell line, WT, IKZF2 (ChIP)
- GSM8887404 EW-1 cell line, WT (Input)
- GSM8887405 EW-1 cell line, WT, POU3F2 (ChIP)
- GSM8887406 EW-1 cell line, WT, SOX2 (ChIP)
- GSM8887407 CHLA-9 cell line, WT, H3K27ac (ChIP)
- GSM8887408 A673/TR/shEF1 cell line, KD, H3K27ac (ChIP)
- GSM8887409 TC-71 cell line, KD, H3K27ac (ChIP)
- GSM8887410 SK-N-MC cell line, KD, H3K27ac (ChIP)
- GSM8887411 MHH-ES-1 cell line, KD, H3K27ac (ChIP)
- GSM8887412 CHLA-9 cell line, WT (Input)
- GSM8887413 SK-N-MC cell line, WT (Input)
- GSM8887414 A673/TR/shEF1 cell line, WT, FLI1 (ChIP)
- GSM8887415 CHLA-9 cell line, WT, FLI1 (ChIP)
- GSM8887416 MSC15 cell line, WT, H3K27ac (ChIP)
- GSM8887417 MSCVL cell line, WT, H3K27ac (ChIP)
- 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, ets, sarcoma
- GSE317136 EWSR1::FLI1 Suppresses Ribosome Biogenesis and Creates a Targetable Vulnerability in Ewing Sarcoma 66 samples same disease briefing · shares ewsr1, sarcoma
- 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 ewsr1, sarcoma
- GSE332630 Multimodal single-cell analyses reveal distinct fusion-regulated transcriptional programs in Ewing sarcoma 22 samples same disease briefing · shares sarcoma
- GSE263234 ARID1A IDR Targets EWS-FLI1 Condensates and Finetunes Productive Chromatin Remodeling 12 samples same disease briefing · shares ets
- GSE270570 Endogenous degron alleles enable tunable control of EWSR1-FLI1 oncoprotein expression 7 samples same disease briefing · shares ewsr1
- GSE176339 The Ewing Sarcoma Cell Line Atlas (ESCLA) 306 samples same disease briefing · shares 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
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.