EWSR1::FLI1 Suppresses Ribosome Biogenesis and Creates a Targetable Vulnerability in Ewing Sarcoma
RNA-seq (gene expression) · human · 66 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
- 66 samples: 22 conditions, mostly in triplicateGroups 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.
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 GSE317136_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: 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 PRJNA1406153 and SRA study SRP665172. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 6 samples read as cases, 6 as controls.
How we read this: 22 replicated groups read from 66 sample titles; they account for 66 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.
- GSM9465570 A-673, polysome-bound, replicate 1 A-673, polysome-bound,
- GSM9465571 A-673, total RNA, replicate 1 A-673, total RNA,
- GSM9465572 A-673, polysome-bound, replicate 2 A-673, polysome-bound,
- GSM9465573 A-673, total RNA, replicate 2 A-673, total RNA,
- GSM9465574 A-673, polysome-bound, replicate 3 A-673, polysome-bound,
- GSM9465575 A-673, total RNA, replicate 3 A-673, total RNA,
- GSM9465576 CHLA-9, polysome-bound, replicate 1 CHLA-9, polysome-bound,
- GSM9465577 CHLA-9, total RNA, replicate 1 CHLA-9, total RNA,
- GSM9465578 CHLA-9, polysome-bound, replicate 2 CHLA-9, polysome-bound,
- GSM9465579 CHLA-9, total RNA, replicate 2 CHLA-9, total RNA,
- GSM9465580 CHLA-9, polysome-bound, replicate 3 CHLA-9, polysome-bound,
- GSM9465581 CHLA-9, total RNA, replicate 3 CHLA-9, total RNA,
- GSM9465582 IMR90, polysome-bound, replicate 1 IMR90, polysome-bound,
- GSM9465583 IMR90, total RNA, replicate 1 IMR90, total RNA,
- GSM9465584 IMR90, polysome-bound, replicate 2 IMR90, polysome-bound,
- GSM9465585 IMR90, total RNA, replicate 2 IMR90, total RNA,
- GSM9465586 IMR90, polysome-bound, replicate 3 IMR90, polysome-bound,
- GSM9465587 IMR90, total RNA, replicate 3 IMR90, total RNA,
- GSM9465588 hMSC, polysome-bound, replicate 1 hMSC, polysome-bound,
- GSM9465589 hMSC, total RNA, replicate 1 hMSC, total RNA,
- GSM9465590 hMSC, polysome-bound, replicate 2 hMSC, polysome-bound,
- GSM9465591 hMSC, total RNA, replicate 2 hMSC, total RNA,
- GSM9465592 hMSC, polysome-bound, replicate 3 hMSC, polysome-bound,
- GSM9465593 hMSC, total RNA, replicate 3 hMSC, total RNA,
- GSM9465594 RH-30, polysome-bound, replicate 1 RH-30, polysome-bound,
- GSM9465595 RH-30, total RNA, replicate 1 RH-30, total RNA,
- GSM9465596 RH-30, polysome-bound, replicate 2 RH-30, polysome-bound,
- GSM9465597 RH-30, total RNA, replicate 2 RH-30, total RNA,
- GSM9465598 RH-30, polysome-bound, replicate 3 RH-30, polysome-bound,
- GSM9465599 RH-30, total RNA, replicate 3 RH-30, total RNA,
- GSM9465600 RD, polysome-bound, replicate 1 RD, polysome-bound,
- GSM9465601 RD, total RNA, replicate 1 RD, total RNA,
- GSM9465602 RD, polysome-bound, replicate 2 RD, polysome-bound,
- GSM9465603 RD, total RNA, replicate 2 RD, total RNA,
- GSM9465604 RD, polysome-bound, replicate 3 RD, polysome-bound,
- GSM9465605 RD, total RNA, replicate 3 RD, total RNA,
- GSM9465606 SK-N-MC, polysome-bound, replicate 1 SK-N-MC, polysome-bound,
- GSM9465607 SK-N-MC, total RNA, replicate 1 SK-N-MC, total RNA,
- GSM9465608 SK-N-MC, polysome-bound, replicate 2 SK-N-MC, polysome-bound,
- GSM9465609 SK-N-MC, total RNA, replicate 2 SK-N-MC, total RNA,
+ 26 more — browse all 66 samples with per-sample file links →
- 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
- 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, fli1
- GSE270570 Endogenous degron alleles enable tunable control of EWSR1-FLI1 oncoprotein expression 7 samples same disease briefing · shares ewsr1, fli1
- 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 fli1
- GSE267223 STAG2 loss in Ewing sarcoma alters enhancer-promoter contacts dependent and independent of EWS::FLI1 52 samples same disease briefing · shares fli1
- 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
- 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
- GSE293632 The hegemonic EWSR1::ETS oncogene overrules core regulatory circuitry mechanisms in Ewing sarcoma. 39 samples same disease briefing · shares ewsr1
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.