The kinase inhibitor GNF-7 is synthetically lethal in topoisomerase 1 deficient Ewing Sarcoma
RNA-seq (gene expression) · human · 29 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
- 29 samples: 29 samples, each with a distinct title — no replicated groupsGroups 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 Kinase Inhibitor GNF-7 Is Synthetically Lethal in Topoisomerase 1-Deficient Ewing SarcomaCancers · 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 GSE298880_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 PRJNA1271555 and SRA study SRP589648. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 29 sample titles: 29 distinct titles with little repetition. 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.
- GSM9025484 EW8 cells, WT, 0h, RepA
- GSM9025485 EW8 cells, WT, 0h, RepB
- GSM9025486 EW8 cells, WT, 4h, RepA
- GSM9025487 EW8 cells, WT, 4h RepB
- GSM9025488 EW8 cells, WT, 8h, RepA
- GSM9025489 EW8 cells, WT, 8h, RepB
- GSM9025490 EW8 cells, WT, 16h, RepA
- GSM9025491 EW8 cells, WT, 16h, RepB
- GSM9025492 EW8 cells, WT, 24h, RepA
- GSM9025493 EW8 cells, WT, 24h, RepB
- GSM9025494 EW8 cells, WT, 48h, RepA
- GSM9025495 EW8 cells, WT, 48h, RepB
- GSM9025496 EW8 cells, WT, 72h, RepA
- GSM9025497 EW8 cells, WT, 72h, RepB
- GSM9025498 EW8 cells, TOP1 KD, 0h, RepA
- GSM9025499 EW8 cells, TOP1 KD, 0h, RepB
- GSM9025500 EW8 cells, TOP1 KD, 0h, RepC
- GSM9025501 EW8 cells, TOP1 KD, 4h, RepA
- GSM9025502 EW8 cells, TOP1 KD, 4h, RepB
- GSM9025503 EW8 cells, TOP1 KD, 8h, RepA
- GSM9025504 EW8 cells, TOP1 KD, 8h, RepB
- GSM9025505 EW8 cells, TOP1 KD, 16h, RepA
- GSM9025506 EW8 cells, TOP1 KD, 16h, RepB
- GSM9025507 EW8 cells, TOP1 KD, 24h, RepA
- GSM9025508 EW8 cells, TOP1 KD, 24h, RepB
- GSM9025509 EW8 cells, TOP1 KD, 48h, RepA
- GSM9025510 EW8 cells, TOP1 KD, 48h, RepB
- GSM9025511 EW8 cells, TOP1 KD, 72h, RepA
- GSM9025512 EW8 cells, TOP1 KD, 72h, RepB
- GSE299432 Transcriptional Rewiring of BET Inhibitor Treated Ewing Sarcoma Cells Augments their Dependency on Focal Adhesion Kinase 30 samples same disease briefing · shares inhibitor, sarcoma, kinase
- GSE279738 A novel combination of CDK4/6 and PI3K inhibitors exhibits highly synergistic activity and translational potential in Ewing sarcoma. 32 samples same disease briefing · shares inhibitor, sarcoma
- GSE280573 Histone deacetylase inhibitors target regulators of DNA replication and the cellular response to DNA replication stress in Ewing sarcoma cells 15 samples same disease briefing · shares inhibitor, sarcoma
- GSE311851 LSD1 Performs Demethylase-Independent and Context-Specific Roles in Ewing Sarcoma 114 samples same disease briefing · shares sarcoma
- GSE299137 Autocrine TGFβ2 enforces a transcriptionally hybrid cell state in Ewing sarcoma 48 samples same disease briefing · shares sarcoma
- GSE338238 Menin inhibition impairs metastatic colonization of Ewing sarcoma 48 samples same disease briefing · shares 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 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 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.