Targeting Ewing sarcoma cells via small molecule YK-4-279 treatment and downregulation of DHX9 helicase [1]
RNA-seq (gene expression) · human · 12 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
- 12 samples: 12 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
- DHX9 helicase impacts on splicing decisions by modulating U2 snRNP recruitment in Ewing sarcoma cellsNucleic acids research · 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 GSE214257_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 PRJNA884647 and SRA study SRP399809. 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 12 sample titles: 12 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.
- GSM6602180 TC-71_DMSO_1 [T1]
- GSM6602181 TC-71_DMSO_2 [T2]
- GSM6602182 TC-71_DMSO_3 [T3]
- GSM6602183 TC-71_YK4279_1 [T4]
- GSM6602184 TC-71_YK4279_2 [T5]
- GSM6602185 TC-71_YK4279_3 [T6]
- GSM6602186 TC-71_scrambled_1 [T7]
- GSM6602187 TC-71_scrambled_2 [T8]
- GSM6602188 TC-71_scrambled_3 [T9]
- GSM6602189 TC-71_siDHX9_1 [T10]
- GSM6602190 TC-71_siDHX9_2 [T11]
- GSM6602191 TC-71_siDHX9_3 [T12]
- GSE301794 Targeting Ewing sarcoma cells via small molecule YK-4-279 treatment and downregulation of DHX9 helicase 12 samples same disease briefing · shares yk-4-279, dhx9, downregulation, targeting, treatment, molecule, helicase, 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
- GSE332586 Mevalonate pathway activation in Ewing sarcoma reveals a 3D-specific synergy between statins and BCL-xL inhibition 36 samples same disease briefing · shares sarcoma
- GSE267222 STAG2 loss in Ewing sarcoma alters enhancer-promoter contacts dependent and independent of EWS::FLI1 32 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.