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Series GSE87112 Query DataSets for GSE87112
Status Public on Nov 15, 2016
Title A Compendium of Chromatin Contact Maps Reveal Spatially Active Regions in the Human Genome
Platform organism Homo sapiens
Sample organisms Homo sapiens; Mus musculus
Experiment type Other
Expression profiling by high throughput sequencing
Third-party reanalysis
Summary The three-dimensional configuration of DNA is integral to all nuclear processes in eukaryotes, yet our knowledge of the chromosome architecture is still limited. Genome-wide chromosome conformation capture studies have uncovered features of chromatin organization in cultured cells, however, genome architecture in human tissues has yet to be explored. Here, we report the most comprehensive survey to date of chromatin organization in human tissues. Through integrative analysis of chromatin contact maps in 21 primary human tissues and cell types, we discover genomic regions that exhibit unusually high levels of local chromatin interactions. These frequently interacting regions (FIREs) are enriched for active enhancers and are located near tissue-specifically expressed genes. Unlike previously identified chromatin loops, FIREs tend to engage in promiscuous local chromatin interactions in a tissue-specific manner. FIRE formation is dependent on the Cohesin complex. Additionally, we show that FIREs can help annotate function of non-coding sequence variants.
 
Overall design The study contains new Hi-C datasets in 11 primary adult tissues. 4 of the 11 tissues have biological replicates, which is defined as two datasets from the same tissue type but from different donor individuals.The study also contains analysis of 3 previously published tissue Hi-C datasets (Leung et al., 2015), as well as several other cell lines from other studies as noted throughout our study. The study also contains the re-analysis and integration of previously published RNA-seq by the Roadmap Epigenomics Consortium (GEO database under accession number GSE16256 and from SRA database under accession umber SRP000941).
all the Hi-C data generated in this study can be visualized in 3dgenome.org
 
Contributor(s) Schmitt AD
Citation(s) 27851967
Submission date Sep 20, 2016
Last update date Mar 20, 2019
Contact name Anthony D Schmitt
E-mail aschmitt1987@gmail.com
Phone 6178429022
Organization name UC San Diego
Department Cellular and Molecular Medicine
Lab Dr. Bing Ren
Street address 9500 GILMAN DR., BLDG. CMME RM 2071
City La Jolla
State/province California
ZIP/Postal code 92037
Country USA
 
Platforms (1)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (19)
GSM2322539 STL002_Adrenal Rep1
GSM2322540 STL001_Bladder Rep1
GSM2322541 STL001_Bladder Rep2
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BioProject PRJNA343608
SRA SRP090175

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
GSE87112_README_pmids.txt.gz 553 b (ftp)(http) TXT
GSE87112_file.tar.gz 36.2 Gb (ftp)(http) TAR
GSE87112_readme.xls.gz 20.3 Kb (ftp)(http) XLS
Processed data is available on Series record
Raw data are available in SRA

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