Cell-of-origin epigenome underlies SS18::SSX-mediated transformation [ChIP-seq]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 27 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
- Mus musculus (mouse)
- Samples
- 27 samples: 27 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 fibroblast epigenome underlies SS18::SSX-mediated transformation in synovial sarcomaNature communications · 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 GSE270369_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 PRJNA1126265 and SRA study SRP515127. 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 27 sample titles: 27 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.
- GSM8340334 tSRC, H3K4me1, ChIP
- GSM8340335 tSRC, H3K4me3, ChIP
- GSM8340336 tSRC, H3K9me3, ChIP
- GSM8340337 tSRC, H3K27me3, ChIP
- GSM8340338 tSRC, H3K36me3, ChIP
- GSM8340339 tSRC, H3K27ac, ChIP
- GSM8340340 tSRC, H3K36me2, ChIP
- GSM8340341 tSRC, H2AK119ub, ChIP
- GSM8340342 tSRC, Input
- GSM8340343 WT, H3K4me1, ChIP
- GSM8340344 WT, H3K4me3, ChIP
- GSM8340345 WT, H3K9me3, ChIP
- GSM8340346 WT, H3K27me3, ChIP
- GSM8340347 WT, H3K36me3, ChIP
- GSM8340348 WT, H3K27ac, ChIP
- GSM8340349 WT, H3K36me2, ChIP
- GSM8340350 WT, H2AK119ub, ChIP
- GSM8340351 WT, Input
- GSM8340352 E12.5, H3K4me1, ChIP
- GSM8340353 E12.5, H3K4me3, ChIP
- GSM8340354 E12.5, H3K9me3, ChIP
- GSM8340355 E12.5, H3K27me3, ChIP
- GSM8340356 E12.5, H3K36me3, ChIP
- GSM8340357 E12.5, H3K27ac, ChIP
- GSM8340358 E12.5, H3K36me2, ChIP
- GSM8340359 E12.5, H2AK119ub, ChIP
- GSM8340360 E12.5, Input
- GSE270370 Cell-of-origin epigenome underlies SS18::SSX-mediated transformation [RNA-seq] 21 samples shares ss18, cell-of-origin, transformation, ssx-mediated, epigenome, underlies
- GSE213265 The fibroblast epigenome underlies SS18::SSX-mediated transformation in synovial sarcoma 7 samples shares ss18, transformation, ssx-mediated, epigenome, underlies
- GSE216769 The fibroblast epigenome underlies SS18::SSX-mediated transformation in synovial sarcoma 18 samples shares ss18, transformation, ssx-mediated, epigenome, underlies
- GSE293598 The Polycomb Protein EED Constrains the SCLC Neuroendocrine Phenotype and Drives Lung Cancer Histological Transformation [ChIP-seq] 27 samples shares transformation, chip-seq
- GSE261741 Identification of epigenetic regulators of fibrotic transformation in cardiac fibroblasts through bulk and single-cell CRISPR screens (ChIP-Seq) 4 samples shares transformation, chip-seq
- GSE269772 SS18::SSX redistributes BAF chromatin remodelers selectively to activate and repress transcription [RNA-Seq] 46 samples shares ss18
- GSE268687 The nBAF complex subunit CREST/SS18L1 regulates hippocampal memory processes via tyrosine 397 and histone acetyltransferase CBP 30 samples shares ss18
- GSE266276 Targeting of SUMOylation leads to cBAF complex stabilization and disruption of the SS18::SSX transcriptome in synovial sarcoma [RNA-seq_Utah] 9 samples shares ss18
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.