Galbase: A comprehensive repository for integrating chicken multi-omics data
Multi-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 resea...
| Main Authors: | , , , , , , , , , , |
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| Format: | Journal Article |
| Language: | Inglés |
| Published: |
Springer
2022
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| Subjects: | |
| Online Access: | https://hdl.handle.net/10568/119618 |
| _version_ | 1855542730671783936 |
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| author | Weiwei Fu Rui Wang Naiyi Xu Jinxin Wang Ran Li Nanaei, H.A. Qinghua Nie Xin Zhao Han Jianlin Ning Yang Yu Jiang |
| author_browse | Han Jianlin Jinxin Wang Naiyi Xu Nanaei, H.A. Ning Yang Qinghua Nie Ran Li Rui Wang Weiwei Fu Xin Zhao Yu Jiang |
| author_facet | Weiwei Fu Rui Wang Naiyi Xu Jinxin Wang Ran Li Nanaei, H.A. Qinghua Nie Xin Zhao Han Jianlin Ning Yang Yu Jiang |
| author_sort | Weiwei Fu |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Multi-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. |
| format | Journal Article |
| id | CGSpace119618 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2022 |
| publishDateRange | 2022 |
| publishDateSort | 2022 |
| publisher | Springer |
| publisherStr | Springer |
| record_format | dspace |
| spelling | CGSpace1196182024-05-01T08:20:06Z Galbase: A comprehensive repository for integrating chicken multi-omics data Weiwei Fu Rui Wang Naiyi Xu Jinxin Wang Ran Li Nanaei, H.A. Qinghua Nie Xin Zhao Han Jianlin Ning Yang Yu Jiang animal breeding chickens genetics indigenous breeds poultry Multi-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. 2022-12 2022-05-23T08:00:03Z 2022-05-23T08:00:03Z Journal Article https://hdl.handle.net/10568/119618 en Open Access Springer Weiwei 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. |
| spellingShingle | animal breeding chickens genetics indigenous breeds poultry Weiwei Fu Rui Wang Naiyi Xu Jinxin Wang Ran Li Nanaei, H.A. Qinghua Nie Xin Zhao Han Jianlin Ning Yang Yu Jiang Galbase: A comprehensive repository for integrating chicken multi-omics data |
| title | Galbase: A comprehensive repository for integrating chicken multi-omics data |
| title_full | Galbase: A comprehensive repository for integrating chicken multi-omics data |
| title_fullStr | Galbase: A comprehensive repository for integrating chicken multi-omics data |
| title_full_unstemmed | Galbase: A comprehensive repository for integrating chicken multi-omics data |
| title_short | Galbase: A comprehensive repository for integrating chicken multi-omics data |
| title_sort | galbase a comprehensive repository for integrating chicken multi omics data |
| topic | animal breeding chickens genetics indigenous breeds poultry |
| url | https://hdl.handle.net/10568/119618 |
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