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ChIP-Atlas is powered by comprehensively integrating all data sets from high-throughput ChIP-seq and DNase-seq, a method for profiling chromatin regions accessible to DNase. In this update, we further collected all the ATAC-seq and whole-genome bisulfite-seq data for six model organisms (human, mouse, rat, fruit fly, nematode, and budding yeast) with the latest genome assemblies. These together with ChIP-seq data can be visualized with the Peak Browser tool and a genome browser to explore the epigenomic landscape of a query genomic locus, such as its chromatin accessibility, DNA methylation status, and protein\u2013genome interactions. This epigenomic landscape can also be characterized for multiple genes and genomic loci by querying with the Enrichment Analysis tool, which, for example, revealed that inflammatory bowel disease-associated SNPs are the most significantly hypo-methylated in neutrophils. Therefore, ChIP-Atlas provides a panoramic view of the whole epigenomic landscape. All datasets are free to download via either a simple button on the web page or an API.<\/jats:p>","DOI":"10.1093\/nar\/gkac199","type":"journal-article","created":{"date-parts":[[2022,3,23]],"date-time":"2022-03-23T12:19:53Z","timestamp":1648037993000},"page":"W175-W182","source":"Crossref","is-referenced-by-count":343,"title":["ChIP-Atlas 2021 update: a data-mining suite for exploring epigenomic landscapes by fully integrating ChIP-seq, ATAC-seq\u00a0and Bisulfite-seq data"],"prefix":"10.1093","volume":"50","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1075-4936","authenticated-orcid":false,"given":"Zhaonan","family":"Zou","sequence":"first","affiliation":[{"name":"Department of Drug Discovery Medicine, Kyoto University Graduate School of Medicine , 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan"},{"name":"Kyoto University Graduate Program for Medical Innovation , Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan"},{"name":"Kyoto University Graduate Division , Yoshida-Nihonmatsu-cho, Sakyo-ku, Kyoto 606-8501, Japan"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3777-5945","authenticated-orcid":false,"given":"Tazro","family":"Ohta","sequence":"additional","affiliation":[{"name":"Database Center for Life Science, Joint Support-Center for Data Science Research, Research Organization of Information and Systems , Yata 1111, Mishima , Shizuoka 411-8540, Japan"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2656-486X","authenticated-orcid":false,"given":"Fumihito","family":"Miura","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, Kyushu University Graduate School of Medical Sciences , 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4767-3259","authenticated-orcid":false,"given":"Shinya","family":"Oki","sequence":"additional","affiliation":[{"name":"Department of Drug Discovery Medicine, Kyoto University Graduate School of Medicine , 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan"},{"name":"Precursory Research for Embryonic Science and Technology, Japan Science and Technology Agency , 4-1-8 Honcho, Kawaguchi , Saitama 332-0012, Japan"}]}],"member":"286","published-online":{"date-parts":[[2022,3,24]]},"reference":[{"key":"2022070500004336300_B1","doi-asserted-by":"crossref","first-page":"1497","DOI":"10.1126\/science.1141319","article-title":"Genome-wide mapping of in vivo protein-DNA interactions","volume":"316","author":"Johnson","year":"2007","journal-title":"Science"},{"key":"2022070500004336300_B2","doi-asserted-by":"crossref","first-page":"311","DOI":"10.1016\/j.cell.2007.12.014","article-title":"High-resolution mapping and characterization of open chromatin across the genome","volume":"132","author":"Boyle","year":"2008","journal-title":"Cell"},{"key":"2022070500004336300_B3","doi-asserted-by":"crossref","first-page":"e46255","DOI":"10.15252\/embr.201846255","article-title":"ChIP-Atlas: a data-mining suite powered by full integration of public chip-seq data","volume":"19","author":"Oki","year":"2018","journal-title":"EMBO Rep."},{"key":"2022070500004336300_B4","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1101\/gad.947102","article-title":"DNA methylation patterns and epigenetic memory","volume":"16","author":"Bird","year":"2002","journal-title":"Genes Dev."},{"key":"2022070500004336300_B5","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1146\/annurev-biochem-052610-091920","article-title":"Programming of DNA methylation patterns","volume":"81","author":"Cedar","year":"2012","journal-title":"Annu. 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