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Small cell carcinoma of the ovary, hypercalcemic type (SCCOHT) cell lines treated with triptolide for 6 or 16h - H3K27ac CUT&RUN

GSE232745 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 56 samples Submitted 2025/01/04 Platform GPL24676
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 56 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
Homo sapiens (human)
Samples
56 samples: 16 conditions, mostly with about 4 replicates eachGroups 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.
Summary (written by the submitters)
Small cell carcinoma of the ovary-hypercalcemic type (SCCOHT) is a rare form of ovarian cancer affecting young women and girls. Survival rates remain poor despite aggressive treatment of these patients with high-dose chemotherapy and radiation. SCCOHT is driven by loss of both SWI/SNF ATPases SMARCA4 and SMARCA2. Loss of SWI/SNF complex activity alters chromatin state, particularly at enhancers, which is believed to be crucial for oncogenesis.
Read the full summary ↓
Super-enhancers are a distinct subset of enhancer clusters frequently associated with oncogenes in cancer. Here we discovered key distinctions between SWI/SNF binding following SMARCA4 restoration at enhancer vs. super-enhancer sites and characterized putative oncogene expression driven by super-enhancer activity. We found high sensitivity of SCCOHT cell lines to triptolide, a small molecule derived from the naturally occurring "thunder god vine" (Tripterygium wilfordii) that targets the XPB subunit of the transcription factor II H (TFIIH) complex, found at super-enhancers. Triptolide inhibits expression of many super-enhancer associated genes, and in particular, oncogenes. Notably, SALL4 expression, which is high in SCCOHT relative to other ovarian cancers and normal cell types, is significantly decreased following short triptolide treatment. In SCCOHT patient-derived xenograft models, triptolide and its prodrug derivative minnelide are particularly effective in inhibiting tumor growth. These results demonstrate the key oncogenic role of super-enhancer activity following epigenetic dysfunction in SCCOHT, which can be effectively targeted through inhibition of its functional components, such as TFIIH inhibition with triptolide.
This dataset
Open GSE232745 in finder → Find more human ChIP / ATAC / CUT&Tag 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 GSE232745_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: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.

Also filed as BioProject PRJNA973684 and SRA study SRP438240. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
16 conditions, mostly with about 4 replicates each
BIN67, Vehicle, 6h, H3K27ac, ×4 BIN67, Triptolide, 6h, H3K27ac, ×4 BIN67, Vehicle, 6h, IgG, ×4 BIN67, Triptolide, 6h, IgG, ×4 COV434, Vehicle, 6h, H3K27ac, ×4 COV434, Triptolide, 6h, H3K27ac, ×4 COV434, Vehicle, 6h, IgG, ×4 COV434, Triptolide, 6h, IgG, ×4 +8 more

Supports a between-group comparison across 56 samples.

How we read this: 16 replicated groups read from 56 sample titles; they account for 56 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.

Samples in this study

+ 16 more — browse all 56 samples with per-sample file links →

Datasets on a similar topic

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