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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Aug 26, 2021 |
| Title |
Genome-wide analysis of enhancer landscape in colorectal cancer subgroups (ChIP-seq) |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Colorectal cancer (CRC) is a highly malignant solid tumor and causes millions of cancer related death worldwide. Here, using H3K27ac chromatin immunoprecipitation followed by sequencing (ChIP-seq) coupled with gene expression data (RNA-seq), we describe the active cis-regulatory landscape across more than seventy diverse CRC patient tissues, including tumor and native tissue. Analysis of the enhancers and super-enhancers with recurrently gained or lost activity revealed novel, clinically relevant insights into CRC biology. Computational reconstruction of core regulatory circuitry identified a master set of transcription factors which is responsible for tumorigenesis and the maintenance of normal intestinal function. Genomic studies have revealed four distinct consensus molecular subgroups (CMS) with divergent biology and clinical behavior and we reveal that differentially regulated enhancers and super-enhancers reinforced inter-subgroup heterogeneity. Our integrated analysis of enhancer elements in a large series of CRC patient paired samples reveals novel insights into cis-regulatory architecture, unrecognized dependencies, and cellular origins.
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| Overall design |
Histone modification profiles (H3K27ac and H3K4me3) of tumor and native tissue from 74 CRC patients were generated by ChIP-seq, using Illumina NovaSeq.
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| Contributor(s) |
Li Q, Lin X, Hu Q, Chen L, Chen M, Li L, Ye M, Wu M |
| Citation(s) |
34737287, 38012744 |
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| Submission date |
Aug 21, 2020 |
| Last update date |
Dec 14, 2023 |
| Contact name |
Qinglan Li |
| E-mail(s) |
liqinglan@whu.edu.cn
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| Organization name |
Wuhan University
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| Street address |
Room 5005, Life Science College, Wuhan University
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| City |
Wuhan City |
| State/province |
Hubei Province |
| ZIP/Postal code |
430062 |
| Country |
China |
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| Platforms (1) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (380)
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| This SubSeries is part of SuperSeries: |
| GSE156614 |
Genome-wide analysis of enhancer landscape in colorectal cancer subgroups |
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| Relations |
| BioProject |
PRJNA658517 |
| SRA |
SRP278372 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE156613_RAW.tar |
86.4 Gb |
(http)(custom) |
TAR (of BED, BW) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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