The goals of the WashU TaRGET Environmental Epigenomics Data Coordination Center (TaRGET T2C DCC) component to the TaRGET Consortium are to collect, store, curate, and display all data, metadata, and analysis tools generated by the TaRGET. The DCC will also assist in the development and dissemination of metadata and standards to be adopted by the community at large, approaches for integrative analysis of a wide-range of data types, and visualization and analysis tools to facilitate access and understanding of complex datasets to non-expert users. Ultimately, the TaRGET Consortium will produce tools, analysis, models, and data that form the reference maps of the environmental exposure related epigenomes of different cells and tissues, and we will develop the DCC into a substantial service organization allowing scientific research to take full advantage of the TaRGET reference maps. To support the TaRGET Consortium, we will establish databases with an application framework to facilitate complex data loading including detailed experimental descriptions and metadata; we will define and establish pipelines that connect all Consortium members to the data, and create avenues of access that distribute the data to the greater biological research community; we will establish metadata requirements, controlled vocabularies, standardized data formats, and quality control metrics for all TaRGET data; we will bring together laboratories that generate complex data types via experimental assays with laboratories that integrate these data using computational tools to define the epigenomic programs in the context of environmental exposure. Through the creation of structures data flow pipelines for the verification and validation of all data, and providing processes for the documentation of metadata, the DCC will enhance the TaRGET data production. The DCC will also coordinate integrative data analysis by creating and adapting analysis pipelines, and by developing advanced Genome Browser functions for the visual integration of TaRGET data. In addition, we will create TaRGET Data Portal that will be the primary entry point to the wealth of experimental data as well as computational analyses. The Portal will integrate these data resources and make them available via enhanced search and browsing capabilities. Finally, the DCC will provide documentation, training, and outreach via many media including written documentation, video tutorials, online books, webinars, and meeting workshops and presentations.
of this work for public health is that comprehensive determination of epigenetic changes associated with environmental exposures in a variety of cell types is essential for understanding the factors, such as the timing of exposure, that influence whether induced changes are conserved across tissues, and to assess the utility of surrogate cell types for epigenetic analyses, and ultimately for environmental healt research.
|Zhang, Chengkang; Lee, Hyung Joo; Shrivastava, Anura et al. (2018) Long-Term In Vitro Expansion of Epithelial Stem Cells Enabled by Pharmacological Inhibition of PAK1-ROCK-Myosin II and TGF-? Signaling. Cell Rep 25:598-610.e5|
|Jiang, Kaiyu; Wong, Laiping; Chen, Yanmin et al. (2018) Soluble inflammatory mediators induce transcriptional re-organization that is independent of dna methylation changes in cultured human chorionic villous trophoblasts. J Reprod Immunol 128:2-8|
|Xing, Xiaoyun; Zhang, Bo; Li, Daofeng et al. (2018) Comprehensive Whole DNA Methylome Analysis by Integrating MeDIP-seq and MRE-seq. Methods Mol Biol 1708:209-246|
|Agrawal, A; Chou, Y-L; Carey, C E et al. (2018) Genome-wide association study identifies a novel locus for cannabis dependence. Mol Psychiatry 23:1293-1302|
|Dai, Xiaoyu; Lin, Nan; Li, Daofeng et al. (2018) A non-randomized procedure for large-scale heterogeneous multiple discrete testing based on randomized tests. Biometrics :|
|Zhu, Liangliang; Yan, Feihu; Wang, Zhen et al. (2018) Genome-wide DNA methylation profiling of primary colorectal laterally spreading tumors identifies disease-specific epimutations on common pathways. Int J Cancer 143:2488-2498|
|Wang, Ting; Pehrsson, Erica C; Purushotham, Deepak et al. (2018) The NIEHS TaRGET II Consortium and environmental epigenomics. Nat Biotechnol 36:225-227|
|Wang, Yanli; Song, Fan; Zhang, Bo et al. (2018) The 3D Genome Browser: a web-based browser for visualizing 3D genome organization and long-range chromatin interactions. Genome Biol 19:151|
|Sundaram, Vasavi; Wang, Ting (2018) Transposable Element Mediated Innovation in Gene Regulatory Landscapes of Cells: Re-Visiting the ""Gene-Battery"" Model. Bioessays 40:|
|Cheng, Cheng; Deng, Pan-Yue; Ikeuchi, Yoshiho et al. (2018) Characterization of a Mouse Model of Börjeson-Forssman-Lehmann Syndrome. Cell Rep 25:1404-1414.e6|
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