Please use this identifier to cite or link to this item: http://bura.brunel.ac.uk/handle/2438/21299
Title: Expanded encyclopaedias of DNA elements in the human and mouse genomes
Authors: Sisu, C
The ENCODE Project Consortium
Weng, Z
Keywords: data integration;epigenomics;functional genomics
Issue Date: 29-Jul-2020
Publisher: Nature Research
Citation: Nature, 2020, 583, 699 – 710
Abstract: © The Author(s) 2020. The human and mouse genomes contain instructions that specify RNAs and proteins and govern the timing, magnitude, and cellular context of their production. To better delineate these elements, phase III of the Encyclopedia of DNA Elements (ENCODE) Project has expanded analysis of the cell and tissue repertoires of RNA transcription, chromatin structure and modification, DNA methylation, chromatin looping, and occupancy by transcription factors and RNA-binding proteins. Here we summarize these efforts, which have produced 5,992 new experimental datasets, including systematic determinations across mouse fetal development. All data are available through the ENCODE data portal (https://www.encodeproject.org), including phase II ENCODE1 and Roadmap Epigenomics2 data. We have developed a registry of 926,535 human and 339,815 mouse candidate cis-regulatory elements, covering 7.9 and 3.4% of their respective genomes, by integrating selected datatypes associated with gene regulation, and constructed a web-based server (SCREEN; http://screen.encodeproject.org) to provide flexible, user-defined access to this resource. Collectively, the ENCODE data and registry provide an expansive resource for the scientific community to build a better understanding of the organization and function of the human and mouse genomes.
Description: All data are available on the ENCODE data portal: www.encodeproject. org. All code is available on GitHub from the links provided in the methods section. Code related to the Registry of cCREs can be found at https:// github.com/weng-lab/ENCODE-cCREs. Code related to SCREEN can be found at https://github.com/weng-lab/SCREEN.
URI: https://bura.brunel.ac.uk/handle/2438/21299
DOI: https://doi.org/10.1038/s41586-020-2493-4
ISSN: 0028-0836
Appears in Collections:Dept of Life Sciences Embargoed Research Papers

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