{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,29]],"date-time":"2026-05-29T20:58:18Z","timestamp":1780088298169,"version":"3.54.0"},"reference-count":38,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2022,9,12]],"date-time":"2022-09-12T00:00:00Z","timestamp":1662940800000},"content-version":"vor","delay-in-days":254,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"the Distinguished Discipline Support Program of Zhejiang University","award":["226-2022-00153"],"award-info":[{"award-number":["226-2022-00153"]}]},{"name":"the Leading Innovative and Entrepreneur Team Introduction Program of Zhejiang","award":["2019R01002"],"award-info":[{"award-number":["2019R01002"]}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32172008"],"award-info":[{"award-number":["32172008"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,9,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The rapid advancement of sequencing technology, including next-generation sequencing (NGS), has greatly improved sequencing efficiency and decreased cost. Consequently, huge amounts of genomic, transcriptomic and epigenetic data concerning cotton species have been generated and released. These large-scale data provide immense opportunities for the study of cotton genomic structure and evolution, population genetic diversity and genome-wide mining of excellent genes for important traits. However, the complexity of NGS data also causes distress, as it cannot be utilized easily. Here, we presented the cotton omics data platform COTTONOMICS (http:\/\/cotton.zju.edu.cn\/), an easily accessible web database that integrates 32.5\u2009TB of omics data including seven assembled genomes, resequencing data from 1180 allotetraploid cotton accessions and RNA-sequencing (RNA-seq), small RNA-sequencing (smRNA-seq), Chromatin Immunoprecipitation sequencing (ChIP-seq), DNase hypersensitive sites sequencing (DNase-seq) and Bisulfite sequencing (BS-seq). COTTONOMICS allows users to employ various search scenarios and retrieve information concerning the cotton genomes, genomic variation (Single nucleotide polymorphisms (SNPs) and Insertion and Deletion (InDels)), gene expression, smRNA expression, epigenetic regulation and quantitative trait locus (QTLs). The user-friendly web interface offers a variety of modules for storing, retrieving, analyzing and visualizing cotton multi-omics data to diverse ends, thereby enabling users to decipher cotton population genetics and identify potential novel genes that influence agronomically beneficial traits.<\/jats:p>\n               <jats:p>Database URL: http:\/\/cotton.zju.edu.cn<\/jats:p>","DOI":"10.1093\/database\/baac080","type":"journal-article","created":{"date-parts":[[2022,9,12]],"date-time":"2022-09-12T16:11:26Z","timestamp":1662999086000},"source":"Crossref","is-referenced-by-count":27,"title":["COTTONOMICS: a comprehensive cotton multi-omics database"],"prefix":"10.1093","volume":"2022","author":[{"given":"Fan","family":"Dai","sequence":"first","affiliation":[{"name":"Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University , Hangzhou, Zhejiang 310058, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiedan","family":"Chen","sequence":"additional","affiliation":[{"name":"Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University , Hangzhou, Zhejiang 310058, China"},{"name":"Tea Research Institute, Chinese Academy of Agricultural Science , Hangzhou 310008, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ziqian","family":"Zhang","sequence":"additional","affiliation":[{"name":"Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University , Hangzhou, Zhejiang 310058, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fengjun","family":"Liu","sequence":"additional","affiliation":[{"name":"Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University , Hangzhou, Zhejiang 310058, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jun","family":"Li","sequence":"additional","affiliation":[{"name":"Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University , Hangzhou, Zhejiang 310058, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ting","family":"Zhao","sequence":"additional","affiliation":[{"name":"Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University , Hangzhou, Zhejiang 310058, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yan","family":"Hu","sequence":"additional","affiliation":[{"name":"Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University , Hangzhou, Zhejiang 310058, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tianzhen","family":"Zhang","sequence":"additional","affiliation":[{"name":"Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University , Hangzhou, Zhejiang 310058, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1546-7645","authenticated-orcid":false,"given":"Lei","family":"Fang","sequence":"additional","affiliation":[{"name":"Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University , Hangzhou, Zhejiang 310058, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2022,9,12]]},"reference":[{"key":"2022091216041742900_R1","doi-asserted-by":"publisher","first-page":"101","DOI":"10.1186\/s12870-017-1039-x","article-title":"CottonFGD: an integrated functional genomics database for cotton","volume":"17","author":"Zhu","year":"2017","journal-title":"BMC Plant Biol."},{"key":"2022091216041742900_R2","doi-asserted-by":"publisher","first-page":"D1090","DOI":"10.1093\/nar\/gkw910","article-title":"ccNET: database of co-expression networks with functional modules for diploid and polyploid Gossypium","volume":"45","author":"You","year":"2017","journal-title":"Nucleic Acids 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