DNA demethylating agents represent a therapeutic opportunity for synovial sarcoma [RNA-Seq 2]
RNA-seq (gene expression) · human · 23 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
- Soft tissue sarcomaThis series is part of our curated briefing on it.
- Samples
- 23 samples: 6 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
- DNA demethylating agents suppress preclinical models of synovial sarcomaThe Journal of clinical investigation · 2025
Read the full summary ↓
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 GSE291312_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 PRJNA1232808 and SRA study SRP568513. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 6 replicated groups read from 23 sample titles; they account for 12 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.
- GSM8833295 HSSY5A1 HSSY5A
- GSM8833296 HSSY5A2 HSSY5A
- GSM8833297 HSSYD1 HSSYD
- GSM8833298 HSSYD2 HSSYD
- GSM8833299 HSSYC1 HSSYC
- GSM8833300 HSSYC2 HSSYC
- GSM8833301 SYO5A1 SYO5A
- GSM8833302 SYO5A2 SYO5A
- GSM8833303 SYOD1 SYOD
- GSM8833304 SYOD2 SYOD
- GSM8833305 SYOC1 SYOC
- GSM8833306 SYOC2 SYOC
- GSM8833307 2467
- GSM8833308 2800
- GSM8833309 2802
- GSM8833310 2803
- GSM8833311 2481
- GSM8833312 2482
- GSM8833313 1388
- GSM8833314 2434
- GSM8833315 1929
- GSM8833316 1467
- GSM8833317 2426
- GSE300974 CDK8 Inhibition Releases the Muscle Differentiation Blockade in Fusion-driven Alveolar Rhabdomyosarcoma [RNA-seq] 30 samples same disease briefing · shares sarcoma, rna-seq
- GSE292872 FANCM is Required for the PAX3::FOXO1-Driven Oncogenic Program in Rhabdomyosarcoma [RNA-Seq] 21 samples same disease briefing · shares sarcoma, rna-seq
- GSE144190 Systematic profiling of synovial sarcoma transcriptome 20 samples same disease briefing · shares synovial, sarcoma
- GSE240287 RNA-sequencing of matched samples from rhabdomyosarcoma samples, obtained before therapy and mid-treatment resection 18 samples same disease briefing · shares sarcoma, rna-seq
- GSE279213 Targeting De Novo Cholesterol Synthesis as a Therapeutic Strategy in Rhabdomyosarcoma 8 samples same disease briefing · shares therapeutic, sarcoma
- GSE131309 Opposing genetic and immune mechanisms shape oncogenic programs in synovial sarcoma 4 samples same disease briefing · shares synovial, sarcoma
- GSE312030 Combined inhibition of HRAS and MEK induces tumor regression and restores myogenic differentiation in HRAS-mutant rhabdomyosarcoma 159 samples same disease briefing · shares sarcoma
- GSE273829 GABA promotes resistance to immunotherapy of patients with TLS-positive tumors [RNA-seq] 92 samples same disease briefing · shares rna-seq
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.