Moore, Jill EJill EMoorePurcaro, Michael JMichael JPurcaroPratt, Henry EHenry EPrattEpstein, Charles BCharles BEpsteinShoresh, NoamNoamShoreshAdrian, JessikaJessikaAdrianKawli, TruptiTruptiKawliDavis, Carrie ACarrie ADavisDobin, AlexanderAlexanderDobinKaul, RajinderRajinderKaulHalow, JessicaJessicaHalowVan Nostrand, Eric LEric LVan NostrandFreese, PeterPeterFreeseGorkin, David UDavid UGorkinShen, YinYinShenHe, YupengYupengHeMackiewicz, MarkMarkMackiewiczPauli-Behn, FlorenciaFlorenciaPauli-BehnWilliams, Brian ABrian AWilliamsMortazavi, AliAliMortazaviKeller, Cheryl ACheryl AKellerZhang, Xiao-OuXiao-OuZhangElhajjajy, Shaimae IShaimae IElhajjajyHuey, JackJackHueyDickel, Diane EDiane EDickelSnetkova, ValentinaValentinaSnetkovaWei, XintaoXintaoWeiWang, XiaofengXiaofengWangRivera-Mulia, Juan CarlosJuan CarlosRivera-MuliaRozowsky, JoelJoelRozowskyZhang, JingJingZhangChhetri, Surya BSurya BChhetriZhang, JialingJialingZhangVictorsen, AlecAlecVictorsenWhite, Kevin PKevin PWhiteVisel, AxelAxelViselYeo, Gene WGene WYeoBurge, Christopher BChristopher BBurgeLécuyer, EricEricLécuyerGilbert, David MDavid MGilbertDekker, JobJobDekkerRinn, JohnJohnRinnMendenhall, Eric MEric MMendenhallEcker, Joseph RJoseph REckerKellis, ManolisManolisKellisKlein, Robert JRobert JKleinNoble, William SWilliam SNobleKundaje, AnshulAnshulKundajeGuigó, RodericRodericGuigóFarnham, Peggy JPeggy JFarnhamCherry, J MichaelJ MichaelCherryMyers, Richard MRichard MMyersRen, BingBingRenGraveley, Brenton RBrenton RGraveleyGerstein, Mark BMark BGersteinPennacchio, Len ALen APennacchioSnyder, Michael PMichael PSnyderBernstein, Bradley EBradley EBernsteinWold, BarbaraBarbaraWoldHardison, Ross CRoss CHardisonGingeras, Thomas RThomas RGingerasStamatoyannopoulos, John AJohn AStamatoyannopoulosWeng, ZhipingZhipingWeng2024-09-022024-09-022020-07-29https://boris-portal.unibe.ch/handle/20.500.12422/36944The 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.en600 - Technology::610 - Medicine & healtharticle10.7892/boris.1461103272824910.1038/s41586-020-2493-4