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Series GSE131953 Query DataSets for GSE131953
Status Public on Aug 08, 2019
Title Comprehensive epigenome characterization reveals the diverse transcriptional regulation across human vascular endothelial cells (ChIP-seq)
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Endothelial cells (ECs) make up the innermost layer throughout the entire vasculature. Their phenotypes and physiological functions are initially regulated by developmental signals and extracellular stimuli. The underlying molecular mechanisms responsible for the diverse phenotypes of ECs from different organs are not well understood.
To characterize the transcriptomic and epigenomic landscape in the vascular system, we cataloged gene expression and active histone marks in nine types of human ECs (generating 148 genome-wide datasets) and carried out a comprehensive analysis with chromatin interaction data. We developed a robust procedure for comparative epigenome analysis that circumvents variations at the level of the individual and technical noise derived from sample preparation under various conditions. Through this approach, we identified 3765 EC-specific enhancers, some of which were associated with disease-associated genetic variations. We also identified various candidate marker genes for each EC type. We found that the nine EC types can be divided into two subgroups, corresponding to those with upper-body origins and lower-body origins, based on their epigenomic landscape. Epigenomic variations were highly correlated with gene expression patterns, but also provided unique information. Most of the deferentially expressed genes and enhancers were cooperatively enriched in more than one EC type, suggesting that the distinct combinations of multiple genes play key roles in the diverse phenotypes across EC types. This comprehensive analysis of epigenome characterization of EC types reveals diverse transcriptional regulation across human vascular systems. These datasets provide a valuable resource for understanding the vascular system and associated diseases.
 
Overall design ChIP-Seq experiments were conducted in human vascular endothelial cells. Fastq files of all samples except for IMR90 have been deposited in the SRA database under accession numbers SRP192924 (BioProject accession: PRJNA532996).
Web link https://rnakato.github.io/HumanEndothelialEpigenome/
 
Contributor(s) Nakato R, Wada Y, Mitsuyama T, Aburatani H, Kimura H, Shirahige K
Citation(s) 31856914
BioProject PRJNA532996
Submission date May 30, 2019
Last update date Dec 23, 2019
Contact name Ryuichiro Nakato
E-mail(s) rnakato@iqb.u-tokyo.ac.jp
Phone +81-3-5841-1471
Organization name The University of Tokyo
Department Institute for Quantitative Biosciences
Lab Laboratory of Computational Genomics
Street address 1-1-1 Yayoi
City Bunkyo-ku
State/province Tokyo
ZIP/Postal code 113-0032
Country Japan
 
Platforms (2)
GPL16558 AB 5500 Genetic Analyzer (Homo sapiens)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (101)
GSM3832542 EC_013_HAoEC ChIP-seq H3K4me3
GSM3832543 EC_013_HAoEC ChIP-seq H3K27ac
GSM3832544 EC_013_HAoEC ChIP-seq Input
Relations
SRA SRP192924

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
GSE131953_EC_ref_enhancer.bed.gz 155.2 Kb (ftp)(http) BED
GSE131953_EC_ref_promoter.bed.gz 67.3 Kb (ftp)(http) BED
GSE131953_RAW.tar 55.0 Gb (http)(custom) TAR (of BED, BW)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
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