GEPREP: A comprehensive data atlas of RNA-seq-based gene expression profiles of exercise responses.

IF 9.7 1区 医学 Q1 HOSPITALITY, LEISURE, SPORT & TOURISM Journal of Sport and Health Science Pub Date : 2024-09-26 DOI:10.1016/j.jshs.2024.100992
Lei Sun, Jinwen Luan, Jinbiao Wang, Xiaoli Li, Wenqian Zhang, Xiaohui Ji, Longhua Liu, Ru Wang, Bingxiang Xu
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Abstract

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.

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GEPREP:基于 RNA-seq 的运动反应基因表达谱综合数据图谱。
背景:体育锻炼可以调节和影响多种组织和细胞的基因表达。最近,随着新一代测序技术的发展,大量基于 RNA 序列(RNA-seq)的体育锻炼基因表达图谱已在公共资源中得到共享;然而,这些图谱的整理和利用率很低。为了解决这个问题,我们通过全面的数据收集、整理和组织,开发了此类数据的数据图集:该数据图谱被称为基于 RNA-seq 的运动反应基因表达谱(GEPREP),它建立在对高质量运动反应 RNA-seq 数据的全面收集之上。每个样本的元数据都经过人工编辑。数据经过统一处理和批次效应校正。所有信息都被精心组织在一个易于使用的网站上,供免费搜索、可视化和下载:GEPREP目前包括69个运动前后的RNA-seq数据集,其中有26个人类数据集(1120个样本)和43个小鼠数据集(1006个样本)。具体来说,有 977 份(87.2%)人类骨骼肌样本和 143 份(12.8%)人类血液样本。此外,还有 9 种小鼠组织的样本,其中骨骼肌(359 个,占 35.7%)和大脑(280 个,占 27.8%)是主要部分。元数据(包括受试者、运动干预、采样地点和后处理方法)也包括在内。元数据和基因表达谱可在 http://www.geprep.org.cn/.Conclusion 免费访问:GEPREP 是基于 RNA-seq 的基因表达图谱的运动反应综合数据图集。它具有可靠的注释和友好的用户界面,有望加深我们对运动生理学的理解。
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来源期刊
CiteScore
18.30
自引率
1.70%
发文量
101
审稿时长
22 weeks
期刊介绍: The Journal of Sport and Health Science (JSHS) is an international, multidisciplinary journal that aims to advance the fields of sport, exercise, physical activity, and health sciences. Published by Elsevier B.V. on behalf of Shanghai University of Sport, JSHS is dedicated to promoting original and impactful research, as well as topical reviews, editorials, opinions, and commentary papers. With a focus on physical and mental health, injury and disease prevention, traditional Chinese exercise, and human performance, JSHS offers a platform for scholars and researchers to share their findings and contribute to the advancement of these fields. Our journal is peer-reviewed, ensuring that all published works meet the highest academic standards. Supported by a carefully selected international editorial board, JSHS upholds impeccable integrity and provides an efficient publication platform. We invite submissions from scholars and researchers worldwide, and we are committed to disseminating insightful and influential research in the field of sport and health science.
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