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

组织、类器官和疾病中的细胞类型和基因组元件目录

基本信息

批准号：
10240019
负责人：
BRADLEY Evan BERNSTEIN
金额：
$ 200.27万
依托单位：
BROAD INSTITUTE, INC.
依托单位国家：
美国
项目类别：
财政年份：
2017
资助国家：
美国
起止时间：
2017-02-01 至 2022-01-31
项目状态：
已结题

项目摘要

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.

项目摘要：NHGRI的编码项目旨在开发功能的全面目录人类基因组中的序列元素。 Encode4的目的是继续催化基因组研究通过捕获新元素并精确定义每个元素作用的细胞和组织类型。对此最后，映射中心将在主要阶段积聚大约1000个潜水员生物样本 encode4。这些样品的优先级用于不同的测定法，以最大化覆盖范围和实用性 Encode4的of是由生物样本工作组领导的持续努力。到主阶段结束时在项目中，我们的映射中心将为染色质状态数据（6个组蛋白标记和CTCF）提供这些生物样本中的306个。在第五年，我们建议将染色质状态数据添加105个额外生物样本。这代表了项目主要阶段的吞吐量增加。此外，我们将来自80个大脑的剖面背侧前额叶皮层（DLPFC），患有不同的阿尔茨海默氏病病理在4年级和第5年，作为独特资金补充的一部分。在第五年，我们将继续绘制染色质状态使用两种技术：Chip-Seq和Mint。已经选择了生物样本以最大程度地与其他映射中心，基因组覆盖率，生物空间的覆盖范围以及百科全书的效用。总结，财团和我们的映射中心继续致力于整体金标准数据集候选功能元素及其细胞环境。为此，编码项目阶段4具有组装了一组关键的生物样本和数据。鉴于已经建立了关键的基础设施，我们的映射中心处于非常高效的操作阶段，而关键的生物样本在手中，通过完成染色质状态，该项目的影响可能在很大程度上是成本效益的放大器在第5年的最高优先信息富含生物样本的映射。

项目成果

期刊论文数量（5）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

A Genetic Variant Associated with Five Vascular Diseases Is a Distal Regulator of Endothelin-1 Gene Expression.

DOI：
10.1016/j.cell.2017.06.049
发表时间：
2017-07-27
期刊：
Cell
影响因子：
64.5
作者：
Gupta RM;Hadaya J;Trehan A;Zekavat SM;Roselli C;Klarin D;Emdin CA;Hilvering CRE;Bianchi V;Mueller C;Khera AV;Ryan RJH;Engreitz JM;Issner R;Shoresh N;Epstein CB;de Laat W;Brown JD;Schnabel RB;Bernstein BE;Kathiresan S
通讯作者：
Kathiresan S

Chromatin complex dependencies reveal targeting opportunities in leukemia.

DOI：
10.1038/s41467-023-36150-7
发表时间：
2023-01-27
期刊：
NATURE COMMUNICATIONS
影响因子：
16.6
作者：
Najm, Fadi J.;DeWeirdt, Peter;Moore, Molly M.;Bevill, Samantha M.;El Farran, Chadi A.;Macias, Kevin A.;Hegde, Mudra;Waterbury, Amanda L.;Liau, Brian B.;van Galen, Peter;Doench, John G.;Bernstein, Bradley E.
通讯作者：
Bernstein, Bradley E.

Analyzing histone ChIP-seq data with a bin-based probability of being signal.