GEO series
Genome-wide maps of chromatin state in 142 cancer cell lines [cell line]
GSE142751
Homo sapiens
Genome binding/occupancy profiling by high throughput sequencing
855 samples
Submitted 2026/07/03
Platform GPL11154
Summary
Epigenetic aberrations are a hallmark of cancer; however, we have limited information on chromatin aberrations present in cancer cells. Here we provide genome-wide maps for histone modification binding for 6 reference histone markers in 145 cancer cell lines belonging to 9 cancer types generating 680 chromatin maps. NMF clustering for H3K27ac-defined enhancers classified cancer cells into 5 distinct subtypes. These subtypes were either correlated with the developmental trajectory of original tissue or cell phenotype such as mesenchymal features. We identify a cluster consisting of different tumor types but with a unique enhancer profile and its dependency on key oncogenes. Detailed characterization of bivalent state switches between cancer cells and their normal counterparts identified epithelial-to-mesenchymal driver transcription factors to be activated via this mechanism in breast, GBM and melanomas. Finally, we identify cancer-specific lengthening of H3K4me3 domains on oncogenes and their shortening on specific tumor-suppressors, respectively. Overall, our study provides epigenome reference maps for widely-used cancer cell lines which will be useful for discovery of important principles about chromatin mediated cancer gene regulation.
This dataset
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Direct links to NCBI, no account and no request form: the whole study as GSE142751_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 855 samples. Raw sequencing reads are also available from ENA.
Also filed as BioProject PRJNA598208 and SRA study SRP239104. Searching any of these in the dataset finder brings you back here.
Study design
40 conditions, each sampled once — no replicated groups
Read from the first 40 of 855 sample titles: 40 distinct titles with little repetition. Check it against the sample list below before relying on it.
Samples in this study
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- GSM4238690 BRCA-B001_H3K4me1_ChIPseq
- GSM4238691 BRCA-B001_H3K9me3_ChIPseq
- GSM4238692 BRCA-B001_H3K27ac_ChIPseq
- GSM4238693 BRCA-B001_H3K79me2_ChIPseq
- GSM4238694 BRCA-B001_H3K4me3_ChIPseq
- GSM4238695 BRCA-B001_H3K27me3_ChIPseq
- GSM4238696 BRCA-B001_Input DNA
- GSM4238697 BRCA-B003_H3K4me1_ChIPseq
- GSM4238698 BRCA-B003_H3K27ac_ChIPseq
- GSM4238699 BRCA-B003_H3K79me2_ChIPseq
- GSM4238700 BRCA-B003_H3K4me3_ChIPseq
- GSM4238701 BRCA-B003_H3K27me3_ChIPseq
- GSM4238702 BRCA-B003_Input DNA
- GSM4238703 BRCA-B008_H3K4me1_ChIPseq
- GSM4238704 BRCA-B008_H3K27ac_ChIPseq
- GSM4238705 BRCA-B008_H3K79me2_ChIPseq
- GSM4238706 BRCA-B008_H3K4me3_ChIPseq
- GSM4238707 BRCA-B008_Input DNA
- GSM4238708 BRCA-B010_H3K4me1_ChIPseq
- GSM4238709 BRCA-B010_H3K27ac_ChIPseq
- GSM4238710 BRCA-B010_H3K79me2_ChIPseq
- GSM4238711 BRCA-B010_H3K4me3_ChIPseq
- GSM4238712 BRCA-B010_Input DNA
- GSM4238713 BRCA-B013_H3K4me1_ChIPseq
- GSM4238714 BRCA-B013_H3K9me3_ChIPseq
- GSM4238715 BRCA-B013_H3K27ac_ChIPseq
- GSM4238716 BRCA-B013_H3K79me2_ChIPseq
- GSM4238717 BRCA-B013_H3K4me3_ChIPseq
- GSM4238718 BRCA-B013_Input DNA
- GSM4238719 BRCA-B014_H3K4me1_ChIPseq
- GSM4238720 BRCA-B014_H3K9me3_ChIPseq
- GSM4238721 BRCA-B014_H3K27ac_ChIPseq
- GSM4238722 BRCA-B014_H3K79me2_ChIPseq
- GSM4238723 BRCA-B014_H3K4me3_ChIPseq
- GSM4238724 BRCA-B014_H3K27me3_ChIPseq
- GSM4238725 BRCA-B014_Input DNA
- GSM4238726 BRCA-B015_H3K4me1_ChIPseq
- GSM4238727 BRCA-B015_H3K9me3_ChIPseq
- GSM4238728 BRCA-B015_H3K27ac_ChIPseq
- GSM4238729 BRCA-B015_H3K79me2_ChIPseq
+ 815 more — browse all 855 samples with per-sample file links →
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