Galbase: A comprehensive repository for integrating chicken multi-omics data

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dc.creatorWeiwei Fu
dc.creatorRui Wang
dc.creatorNaiyi Xu
dc.creatorJinxin Wang
dc.creatorRan Li
dc.creatorNanaei, H.A.
dc.creatorQinghua Nie
dc.creatorXin Zhao
dc.creatorHan Jianlin
dc.creatorNing Yang
dc.creatorYu Jiang
dc.date2022-12
dc.date2022-05-23T08:00:03Z
dc.date2022-05-23T08:00:03Z
dc.date.accessioned2026-06-27T17:19:21Z
dc.descriptionMulti-omics data can provide a stereoscopic view to explore potential causal variations and genes, as well as underlying genetic mechanisms of complex traits. However, for many non-mammalian species, including chickens, these resources are poorly integrated and reused, greatly limiting genetic research and breeding processes of the species.Here, we constructed Galbase, an easily accessible repository that integrates public chicken multi-omics data from 928 re-sequenced genomes, 429 transcriptomes, 379 epigenomes, 15,275 QTL entries, and 7,526 associations. A total of 21.67 million SNPs, 2.71 million InDels, and 488,583 cis-regulatory elements were included. Galbase allows users to retrieve genomic variations in geographical maps, gene expression profiling in heatmaps, and epigenomic signals in peak patterns. It also provides modules for batch annotation of genes, regions, and loci based on multi-layered omics data. Additionally, a series of convenient tools, including the UCSC Genome Browser, WashU Epigenome Browser, BLAT, BLAST, and LiftOver, were also integrated to facilitate search, visualization, and analysis of sequence features.Galbase grants new opportunities to research communities to undertake in-depth functional genomic studies on chicken. All features of Galbase make it a useful resource to identify genetic variations responsible for chicken complex traits. Galbase is publicly available at http://animal.nwsuaf.edu.cn/ChickenVar.
dc.identifierhttps://hdl.handle.net/10568/119618
dc.identifier.urihttp://hdl.handle.net/123456789/148824
dc.languageen
dc.publisherSpringer
dc.rightsOpen Access
dc.sourceWeiwei Fu, Rui Wang, Naiyi Xu, Jinxin Wang, Ran Li, Nanaei, H.A., Qinghua Nie, Xin Zhao, Jianlin Han, Ning Yang and Yu Jiang. 2022. Galbase: A comprehensive repository for integrating chicken multi-omics data. BMC Genomics 23:364.
dc.subjectanimal breeding
dc.subjectchickens
dc.subjectgenetics
dc.subjectindigenous breeds
dc.subjectpoultry
dc.titleGalbase: A comprehensive repository for integrating chicken multi-omics data
dc.typeJournal Article

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Instituto Internacional de Investigaciones Pecuarias (ILRI)