A Catalog of Cell Types and Genomic Elements in Tissues, Organoids and Disease

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Project Summary: NHGRI’s ENCODE Project aims to develop a comprehensive catalog of functional sequence elements in the human genome. The goal of ENCODE4 is to continue to catalyze genome research by capturing new elements and precisely defining the cell & tissue type(s) in which each element acts. To this end, the mapping centers will have amassed approximately 1000 diverse BioSamples during the main phase of ENCODE4. The prioritization of these samples for the different assays to maximize the coverage and utility of ENCODE4 has been an ongoing effort led by the BioSamples working group. By the end of the main phase of the project, our mapping center will have contributed chromatin state data (6 histone marks and CTCF) for 306 of these BioSamples. In year 5, we propose to add chromatin state data for 105 additional BioSamples. This represents an increased throughput from the main phase of the project. In addition, we will profile dorsolateral prefrontal cortex (DLPFC) from 80 brains with varying Alzheimer’s disease pathologies across year 4 and 5 as part of a distinct funding supplement. In year 5, we will continue to map chromatin state using two technologies: ChIP-seq and MINT. BioSamples have been chosen to maximize integration with other mapping centers, genomic coverage, coverage of biological space, and utility of the Encyclopedia. In summary, the consortium and our mapping center continue to work towards a holistic gold-standard dataset of candidate functional elements and their cellular contexts. To this end, the ENCODE project phase 4 has assembled a critical set of BioSamples and data. Given that critical infrastructure has been established, that our mapping center is in a phase of extremely efficient operation, and that key BioSamples are in hand, the impact of the project could be cost-effectively amplified to a great extent by completing chromatin state mapping of the highest priority information-rich BioSamples in Year 5.