PAGES: Physical Activity Genomics, Epigenomics/transcriptomics Site

页数：身体活动基因组学、表观基因组学/转录组学网站

• 批准号: 10318109
• 负责人: STUART C. SEALFON
• 金额: $ 262.41万
• 依托单位: ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI
• 依托单位国家: 美国
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-12-08 至 2024-11-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10318109
• 关键词: ATAC-seq; Area; Bioinformatics; Biological Assay; Budgets; ChIP-seq; Chemicals; Chromatin; Clinical Research; Collaborations; Cost efficiency; Data; Data Analyses; Data Storage and Retrieval; Databases; Deposition; Development; Disease; Elements; Foundations; Funding; Genetic; Genome; Genomics; Goals; Health; Human; Individual; Infrastructure; Institutes; Knowledge; Lead; Metadata; Methods; Modeling; Molecular; Molecular Analysis; New York; Ontology; Pathway interactions; Physical activity; Pilot Projects; Prevention; Production; Protocols documentation; Rat Strains; Rattus; Research Activity; Risk Factors; Sampling; Scientist; Site; Tissue Sample; Tissues; Training; Training Activity; Transducers; Universities; Validation; Work; analysis pipeline; base; bisulfite sequencing; data exchange; data resource; epigenomics; exercise intervention; experience; fitness; gene product; genome sequencing; high throughput analysis; human data; human disease; improved; individual response; insight; machine learning algorithm; medical schools; methylome; mortality risk; predictive modeling; prevent; programs; public database; response; sedentary; success; transcriptome; transcriptome sequencing; transcriptomics; web page; web portal; whole genome

Project Summary Physical activity (PA) prevents or ameliorates a large number of diseases, and inactivity is the 4th leading global mortality risk factor. The molecular mechanisms responsible for the diverse benefits of PA are not well understood. The Molecular Transducers of Physical Activity Consortium (MoTrPAC) is being formed to advance knowledge in this area. We propose to establish PAGES, a Physical Activity Genomics, Epigenomics/transcriptomics Site as an integral component of the MoTrPAC. PAGES will conduct comprehensive analyses of the rat and human PA intervention MoTrPAC samples, contribute these data to public databases, help identify candidate molecular transducers of PA and elucidate new PA response mechanisms, and help develop predictive models of the individual response to PA. PAGES assay sites at Icahn School of Medicine at Mount Sinai, New York Genome Center and Broad Institute provide the infrastructure, expertise and experience to support this large scale, comprehensive analysis of molecular changes associated with PA. PAGES aims are to 1. Work with the MoTrPAC Steering Committee in Year 1 to finalize plans and protocols; 2. Perform assays and analyses to help Identify candidate molecular transducers of the response to PA in rat models and the pathways responsible for model differences, including high-depth RNA-seq and Whole Genome Bisulfite Sequencing (WGBS), supplemented by additional assay types such as ChIP-seq, ATAC-seq based on initial results; 3. Perform comprehensive assays and analyses of the human MoTrPAC clinical study tissue samples, including RNA-seq, WGBS, H3K27ac ChIP-seq, ATAC-seq and whole genome sequencing. 4. Collaborate with the MoTrPAC to analyze data from PAGES and other MoTrPAC analysis sites to identify candidate PA transducers and molecular mechanisms, and to develop predictive models of PA capacity and response to training. The success of PAGES and the MoTrPAC program will transform insight into the molecular networks that transduce PA into health, create an unparalleled comprehensive public PA data resource, and can provide the foundation for profound advances in the prevention and treatment of many major human diseases.

项目总结

项目成果

Transcriptome variation in human tissues revealed by long-read sequencing.

长阅读测序揭示了人体组织中的转录组变化。

• DOI: 10.1038/s41586-022-05035-y
• 发表时间: 2022-08
• 期刊: NATURE
• 影响因子: 64.8
• 作者: Glinos, Dafni A.;Garborcauskas, Garrett;Hoffman, Paul;Ehsan, Nava;Jiang, Lihua;Gokden, Alper;Dai, Xiaoguang;Aguet, Francois;Brown, Kathleen L.;Garimella, Kiran;Bowers, Tera;Costello, Maura;Ardlie, Kristin;Jian, Ruiqi;Tucker, Nathan R.;Ellinor, Patrick T.;Harrington, Eoghan D.;Tang, Hua;Snyder, Michael;Juul, Sissel;Mohammadi, Pejman;MacArthur, Daniel G.;Lappalainen, Tuuli;Cummings, Beryl
• 通讯作者: Cummings, Beryl

DataRemix: a universal data transformation for optimal inference from gene expression datasets.

DataRemix：一种通用数据转换，用于从基因表达数据集中进行最佳推理。

• DOI: 10.1093/bioinformatics/btaa745
• 发表时间: 2021
• 期刊: Bioinformatics (Oxford, England)
• 作者: Mao,Weiguang;Rahimikollu,Javad;Hausler,Ryan;Chikina,Maria
• 通讯作者: Chikina,Maria

A micromachined force sensing apparatus and method for human engineered cardiac tissue and induced pluripotent stem cell characterization.

用于人体工程心脏组织和诱导多能干细胞表征的微机械力传感装置和方法。

• DOI: 10.1016/j.sna.2021.112874
• 发表时间: 2021
• 期刊: Sensors and actuators. A, Physical
• 作者: Turnbull,IreneC;Zhu,Weibin;Stillitano,Francesca;Chien,Chen-Chi;Gaitas,Angelo
• 通讯作者: Gaitas,Angelo

Dissecting aortic aneurysm in Marfan syndrome is associated with losartan-sensitive transcriptomic modulation of aortic cells.

• DOI: 10.1172/jci.insight.168793
• 发表时间: 2023-05-22
• 期刊: JCI INSIGHT
• 影响因子: 8
• 作者: Sun, Yifei;Asano, Keiichi;Sedes, Lauriane;Cantalupo, Anna;Hansen, Jens;Iyengar, Ravi;Walsh, Martin J.;Ramirez, Francesco
• 通讯作者: Ramirez, Francesco