Pig-eRNAdb: a comprehensive enhancer and eRNA dataset of pigs
Abstract Enhancers and the enhancer RNAs (eRNAs) have been strongly implicated in regulations of transcriptions. Based the multi-omics data (ATAC-seq, ChIP-seq and RNA-seq) from public databases, Pig-eRNAdb is a dataset that comprehensively integrates enhancers and eRNAs for pigs using the machine l...
| Main Authors: | , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Nature Portfolio
2024-02-01
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| Series: | Scientific Data |
| Online Access: | https://doi.org/10.1038/s41597-024-02960-7 |
| _version_ | 1797275894172090368 |
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| author | Yifei Wang Weiwei Jin Xiangchun Pan Weili Liao Qingpeng Shen Jiali Cai Wentao Gong Yuhan Tian Dantong Xu Yipeng Li Jiaqi Li Jing Gong Zhe Zhang Xiaolong Yuan |
| author_facet | Yifei Wang Weiwei Jin Xiangchun Pan Weili Liao Qingpeng Shen Jiali Cai Wentao Gong Yuhan Tian Dantong Xu Yipeng Li Jiaqi Li Jing Gong Zhe Zhang Xiaolong Yuan |
| author_sort | Yifei Wang |
| collection | DOAJ |
| description | Abstract Enhancers and the enhancer RNAs (eRNAs) have been strongly implicated in regulations of transcriptions. Based the multi-omics data (ATAC-seq, ChIP-seq and RNA-seq) from public databases, Pig-eRNAdb is a dataset that comprehensively integrates enhancers and eRNAs for pigs using the machine learning strategy, which incorporates 82,399 enhancers and 37,803 eRNAs from 607 samples across 15 tissues of pigs. This user-friendly dataset covers a comprehensive depth of enhancers and eRNAs annotation for pigs. The coordinates of enhancers and the expression patterns of eRNAs are downloadable. Besides, thousands of regulators on eRNAs, the target genes of eRNAs, the tissue-specific eRNAs, and the housekeeping eRNAs are also accessible as well as the sequence similarity of eRNAs with humans. Moreover, the tissue-specific eRNA-trait associations encompass 652 traits are also provided. It will crucially facilitate investigations on enhancers and eRNAs with Pig-eRNAdb as a reference dataset in pigs. |
| first_indexed | 2024-03-07T15:20:34Z |
| format | Article |
| id | doaj.art-06c11b370cc544abb6f3eb04a7072341 |
| institution | Directory Open Access Journal |
| issn | 2052-4463 |
| language | English |
| last_indexed | 2024-03-07T15:20:34Z |
| publishDate | 2024-02-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Data |
| spelling | doaj.art-06c11b370cc544abb6f3eb04a70723412024-03-05T17:39:02ZengNature PortfolioScientific Data2052-44632024-02-011111810.1038/s41597-024-02960-7Pig-eRNAdb: a comprehensive enhancer and eRNA dataset of pigsYifei Wang0Weiwei Jin1Xiangchun Pan2Weili Liao3Qingpeng Shen4Jiali Cai5Wentao Gong6Yuhan Tian7Dantong Xu8Yipeng Li9Jiaqi Li10Jing Gong11Zhe Zhang12Xiaolong Yuan13Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural UniversityHubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural UniversityGuangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural UniversityGuangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural UniversityGuangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural UniversityGuangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural UniversityGuangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural UniversityGuangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural UniversityGuangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural UniversityGuangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural UniversityGuangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural UniversityHubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural UniversityGuangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural UniversityGuangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural UniversityAbstract Enhancers and the enhancer RNAs (eRNAs) have been strongly implicated in regulations of transcriptions. Based the multi-omics data (ATAC-seq, ChIP-seq and RNA-seq) from public databases, Pig-eRNAdb is a dataset that comprehensively integrates enhancers and eRNAs for pigs using the machine learning strategy, which incorporates 82,399 enhancers and 37,803 eRNAs from 607 samples across 15 tissues of pigs. This user-friendly dataset covers a comprehensive depth of enhancers and eRNAs annotation for pigs. The coordinates of enhancers and the expression patterns of eRNAs are downloadable. Besides, thousands of regulators on eRNAs, the target genes of eRNAs, the tissue-specific eRNAs, and the housekeeping eRNAs are also accessible as well as the sequence similarity of eRNAs with humans. Moreover, the tissue-specific eRNA-trait associations encompass 652 traits are also provided. It will crucially facilitate investigations on enhancers and eRNAs with Pig-eRNAdb as a reference dataset in pigs.https://doi.org/10.1038/s41597-024-02960-7 |
| spellingShingle | Yifei Wang Weiwei Jin Xiangchun Pan Weili Liao Qingpeng Shen Jiali Cai Wentao Gong Yuhan Tian Dantong Xu Yipeng Li Jiaqi Li Jing Gong Zhe Zhang Xiaolong Yuan Pig-eRNAdb: a comprehensive enhancer and eRNA dataset of pigs Scientific Data |
| title | Pig-eRNAdb: a comprehensive enhancer and eRNA dataset of pigs |
| title_full | Pig-eRNAdb: a comprehensive enhancer and eRNA dataset of pigs |
| title_fullStr | Pig-eRNAdb: a comprehensive enhancer and eRNA dataset of pigs |
| title_full_unstemmed | Pig-eRNAdb: a comprehensive enhancer and eRNA dataset of pigs |
| title_short | Pig-eRNAdb: a comprehensive enhancer and eRNA dataset of pigs |
| title_sort | pig ernadb a comprehensive enhancer and erna dataset of pigs |
| url | https://doi.org/10.1038/s41597-024-02960-7 |
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