GEO series

SS18::SSX redistributes BAF chromatin remodelers selectively to activate and repress transcription [RNA-Seq]

GSE269772 Mus musculus (mouse) RNA-seq (gene expression) 46 samples Submitted 2025/06/10 Platform GPL34328

At a glance

RNA-seq (gene expression) · mouse · 46 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: Mus musculus (mouse)
Samples: 46 samples
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: Synovial sarcoma reprograms transcription by GBAF activation of polycomb targets and loss of CBAF enhancersNature communications · 2025

Summary (written by the submitters)

Synovial sarcoma (SS) is a rare malignancy, involves a t(X;18) chromosomal translocation that creates a fusion gene SS18-SSX. SS18 is a chromatin remodeling BAF-complexes component, which incorporated in CBAF and GBAF (non-canonical ncBAF). Our previous studies determined that incorporation of the fusion oncoprotein caused degradation of CBAF complexes, emphasizing a critical oncogenic function of GBAF and PBAF in synovial sarcomagenesis.

Read the full summary ↓

To determine the SyS dependencies on different subtypes of BAF complexes during tumor development in vivo, we used our SyS mouse model combined with genetic disruption of specific BAF complexes components ARID1A/B or PBRM1. In this study, our fundings suggest that depletion of ARID1A and ARID1B sped tumorigenesis, without significant change in the histomorphology of the developing tumors. Loss of PBRM1 also led to faster tumor growing, but Pbrm1-silenced tumors lacked the full array of SyS histomorphologies observed in wildtype tumors. Overall, Arid1a or Arid1b disruption rendered tumor transcriptomes that clustered within the hSS2 tumor transcriptomes, unlike Pbrm1 disrupted tumors.

Published in

Synovial sarcoma reprograms transcription by GBAF activation of polycomb targets and loss of CBAF enhancers

Li J, Li L, Smith-Fry K et al. · Nature communications 2025 · PMID 41423472 · doi:10.1038/s41467-025-67841-y

This dataset

Open GSE269772 in finder → Find more mouse RNA-seq datasets →

Download · which file do I need?

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.

1 · Just have a look

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.

Series matrix ↓

2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE269772_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓

3 · Start from the raw reads

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.

Raw reads on ENA ↗

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 PRJNA1123667 and SRA study SRP513763. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41423472) ↗

Samples in this study

The sample list for this study is not cached yet. Press Load samples and it will be fetched from NCBI.

+ 46 more — browse all 46 samples with per-sample file links →

Datasets on a similar topic

GSE269773 SS18::SSX redistributes BAF chromatin remodelers selectively to activate and repress transcription [scRNA-Seq] 5 samples shares ss18, ssx, baf, redistributes, transcription, selectively, remodelers, chromatin
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, ssx, baf
GSE284165 Reorganization of PBAF/cBAF remodelers on H3.3 chromatin regulates BMAL1 activity in the absence of circadian negative feedback 47 samples shares baf, remodelers, chromatin
GSE268687 The nBAF complex subunit CREST/SS18L1 regulates hippocampal memory processes via tyrosine 397 and histone acetyltransferase CBP 30 samples shares ss18, baf
GSE270370 Cell-of-origin epigenome underlies SS18::SSX-mediated transformation [RNA-seq] 21 samples shares ss18, ssx
GSE216769 The fibroblast epigenome underlies SS18::SSX-mediated transformation in synovial sarcoma 18 samples shares ss18, ssx
GSE270369 Cell-of-origin epigenome underlies SS18::SSX-mediated transformation [ChIP-seq] 27 samples shares ss18, ssx
GSE213265 The fibroblast epigenome underlies SS18::SSX-mediated transformation in synovial sarcoma 7 samples shares ss18, ssx

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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.