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Series GSE136888 Query DataSets for GSE136888
Status Public on May 22, 2021
Title ChIP-seq dataset for epigenomics landscape of colorectal cancer
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Cancer cells utilize genetic and epigenetic aberrations for their excessive growth. Although we have sufficient understanding of the genomic alterations in colorectal cancer, we have incomplete knowledge of epigenomic aberrations and their impact on tumor growth. In order to comprehensively define the epigenetic patterns specific to colorectal cancer, we generated profiles for 6 histone modification marks, including H3K4me1 (enhancer), H3K27Ac (active enhancer), H3K9me3 (heterochromatin), H3K27me3 (polycomb repression), H3K79me2 (transcription) and H3K4me3 (promoter), using a high-throughput ChIP-Seq methodology developed in house applicable to frozen tumors. Chromatin state transitions specifically pointed to drastic changes in enhancer patterns, consistent with some prior studies. Furthermore, we identified the best combinatorial chromatin states that could most efficiently distinguish and predict CRC from normal colon. In a more detailed investigation into patterns of active enhancers using normal colon, adenomas and colorectal cancers, we identified specific changes in enhancers from normal tissue to these neoplastic lesions. Importantly, we noted gains of enhancers in a large number of genomic loci in colon cancer compared to adjacent normal tissues. In summary, we have identified aberrant enhancer gains as a major feature of colorectal cancer and propose this to be utilized as a therapeutic approach.
 
Overall design ChIP-seq samples across six different marks -- H3K4me1 (n = 32; 16 Normal and 16 Tumor), H3K9me3 (n = 30 samples; 14 Normal and 16 Tumor), H3K27ac (n = 68 samples; 15 Normal, 34 Tumor, 4 FAPP Normal, 4 Adenoma and 11 CCLE cell lines), H3K79me2 (n = 31 samples; 17 normal and 14 Tumor), H3K4me3 (n = 33 samples; 17 Normal and 16 Tumor) and H3K27me3 (n = 29; 14 normal and 15 Tumor).
 
Contributor(s) Orouji E, Raman AT, Singh AK, Rai K
Citation(s) 34059508
Submission date Sep 04, 2019
Last update date Jun 02, 2021
Contact name Ayush T Raman
E-mail(s) aayushraman09@gmail.com
Organization name Broad Institute of MIT and Harvard
Department Epigenomics Program
Street address 75 Ames St
City Cambridge
State/province MA
ZIP/Postal code 02142
Country USA
 
Platforms (1)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (293)
GSM4060921 SW480 Cell line H3K27ac ChIP-seq
GSM4060922 SW480 Cell line Input ChIP-seq
GSM4060923 SW837 Cell line H3K27ac ChIP-seq
This SubSeries is part of SuperSeries:
GSE136889 Epigenomics landscape of colorectal cancer
Relations
BioProject PRJNA563925
SRA SRP220374

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE136888_RAW.tar 103.9 Mb (http)(custom) TAR (of BED)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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