Background Physical activity can regulate and affect gene expression in multiple tissues and cells.Recently,with the development of next-generation sequencing,a large number of RNA-sequencing(RNA-seq)-based gene expre...Background Physical activity can regulate and affect gene expression in multiple tissues and cells.Recently,with the development of next-generation sequencing,a large number of RNA-sequencing(RNA-seq)-based gene expression profiles about physical activity have been shared in public resources;however,they are poorly curated and underutilized.To tackle this problem,we developed a data atlas of such data through comprehensive data collection,curation,and organization.Methods The data atlas,termed gene expression profiles of RNA-seq-based exercise responses(GEPREP),was built on a comprehensive collection of high-quality RNA-seq data on exercise responses.The metadata of each sample were manually curated.Data were uniformly processed and batch effects corrected.All the information was well organized in an easy-to-use website for free search,visualization,and download.Results GEPREP now includes 69 RNA-seq datasets of pre-and post-exercise,comprising 26 human datasets(1120 samples)and 43 mouse datasets(1006 samples).Specifically,there were 977(87.2%)human samples of skeletal muscle and 143(12.8%)human samples of blood.There were also samples across 9 mice tissues with skeletal muscle(359,35.7%)and brain(280,27.8%)accounting for the main fractions.Metadata—including subject,exercise interventions,sampling sites,and post-processing methods—are also included.The metadata and gene expression profiles are freely accessible at http://www.geprep.org.cn/.Conclusion GEPREP is a comprehensive data atlas of RNA-seq-based gene expression profiles responding to exercise.With its reliable annotations and user-friendly interfaces,it has the potential to deepen our understanding of exercise physiology.展开更多
基金supported by grants from the Shanghai“Science and Technology Innovation Action Plan”Social Development Science and Technology Reach Project(22dz1204600)Shanghai Sports Science and Technology Program(24C002)+2 种基金the National Key R&D Program of China(2020YFA0803800)the National Natural Science Foundation of China(32200515,32271226)Shanghai Municipal Science and Technology Committee of Shanghai outstanding academic leaders plan(21XD1403200).
文摘Background Physical activity can regulate and affect gene expression in multiple tissues and cells.Recently,with the development of next-generation sequencing,a large number of RNA-sequencing(RNA-seq)-based gene expression profiles about physical activity have been shared in public resources;however,they are poorly curated and underutilized.To tackle this problem,we developed a data atlas of such data through comprehensive data collection,curation,and organization.Methods The data atlas,termed gene expression profiles of RNA-seq-based exercise responses(GEPREP),was built on a comprehensive collection of high-quality RNA-seq data on exercise responses.The metadata of each sample were manually curated.Data were uniformly processed and batch effects corrected.All the information was well organized in an easy-to-use website for free search,visualization,and download.Results GEPREP now includes 69 RNA-seq datasets of pre-and post-exercise,comprising 26 human datasets(1120 samples)and 43 mouse datasets(1006 samples).Specifically,there were 977(87.2%)human samples of skeletal muscle and 143(12.8%)human samples of blood.There were also samples across 9 mice tissues with skeletal muscle(359,35.7%)and brain(280,27.8%)accounting for the main fractions.Metadata—including subject,exercise interventions,sampling sites,and post-processing methods—are also included.The metadata and gene expression profiles are freely accessible at http://www.geprep.org.cn/.Conclusion GEPREP is a comprehensive data atlas of RNA-seq-based gene expression profiles responding to exercise.With its reliable annotations and user-friendly interfaces,it has the potential to deepen our understanding of exercise physiology.
