RT Journal Article
SR Electronic
T1 OCHROdb: a comprehensive, quality checked database of open chromatin regions from sequencing data
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 484840
DO 10.1101/484840
A1 Parisa Shooshtari
A1 Samantha Feng
A1 Viswateja Nelakuditi
A1 Justin Foong
A1 Michael Brudno
A1 Chris Cotsapas
YR 2018
UL http://biorxiv.org/content/early/2018/12/03/484840.abstract
AB International consortia, including ENCODE, Roadmap Epigenomics, Genomics of Gene Regulation and Blueprint Epigenome have made large-scale datasets of open chromatin regions publicly available. While these datasets are extremely useful for studying mechanisms of gene regulation in disease and cell development, they only identify open chromatin regions in individual samples. A uniform comparison of accessibility of the same regulatory sites across multiple samples is necessary to correlate open chromatin accessibility and expression of target genes across matched cell types. Additionally, although replicate samples are available for majority of cell types, a comprehensive replication-based quality checking of individual regulatory sites is still lacking. We have integrated 828 DNase-I hypersensitive sequencing samples, which we have uniformly processed and then clustered their regulatory regions across all samples. We checked the quality of open-chromatin regions using our replication test. This has resulted in a comprehensive, quality-checked database of Open CHROmatin (OCHROdb) regions for 194 unique human cell types and cell lines which can serve as a reference for gene regulatory studies involving open chromatin. We have made this resource publicly available: users can download the whole database, or query it for their genomic regions of interest and visualize the results in an interactive genome browser.