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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

Feb 22, 2021

Contact name

Anthony D Schmitt

E-mail(s)

[email protected]

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)

More...

GSM2322539	STL002_Adrenal Rep1
GSM2322540	STL001_Bladder Rep1
GSM2322541	STL001_Bladder Rep2

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BioProject

SRA

Download family	Format
SOFT formatted family file(s)	SOFT
MINiML formatted family file(s)	MINiML
Series Matrix File(s)	TXT

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
SRA Run Selector
Processed data are available on Series record
Raw data are available in SRA