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

> **NIH NIH UM1** · BROAD INSTITUTE, INC. · 2021 · $2,002,687

## Abstract

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.

## Key facts

- **NIH application ID:** 10240019
- **Project number:** 3UM1HG009390-04S1
- **Recipient organization:** BROAD INSTITUTE, INC.
- **Principal Investigator:** BRADLEY Evan BERNSTEIN
- **Activity code:** UM1 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $2,002,687
- **Award type:** 3
- **Project period:** 2017-02-01 → 2022-01-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10240019

## Citation

> US National Institutes of Health, RePORTER application 10240019, A Catalog of Cell Types and Genomic Elements in Tissues, Organoids and Disease (3UM1HG009390-04S1). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/10240019. Licensed CC0.

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