Proteomics

Dataset Information

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The EN-TEx Resource for Personal Functional Genomics

ABSTRACT: An overall goal of functional genomics has been to measure the impact of variants on molecular endophenotypes (e.g. gene expression levels or the degree of TF binding) and relate this to organismal traits and disease phenotypes. However, all the experiments to date have been described relative to a generic reference genome, significantly hobbling their interpretation. Here, we describe a strategy for finding significant relationships between disease variation and genomic annotation via personal functional genomics, by performing personal genome sequencing and paired functional genomics experiments, on the same individual.

INSTRUMENT(S): Orbitrap Fusion

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Spleen, Testis, Prostate Gland, Liver, Small Intestine

SUBMITTER: James Wright  

LAB HEAD: Jyoti Choudhary

PROVIDER: PXD022787 | Pride | 2024-05-22

REPOSITORIES: Pride

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Publications

The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models.

Rozowsky Joel J   Gao Jiahao J   Borsari Beatrice B   Yang Yucheng T YT   Galeev Timur T   Gürsoy Gamze G   Epstein Charles B CB   Xiong Kun K   Xu Jinrui J   Li Tianxiao T   Liu Jason J   Yu Keyang K   Berthel Ana A   Chen Zhanlin Z   Navarro Fabio F   Sun Maxwell S MS   Wright James J   Chang Justin J   Cameron Christopher J F CJF   Shoresh Noam N   Gaskell Elizabeth E   Drenkow Jorg J   Adrian Jessika J   Aganezov Sergey S   Aguet François F   Balderrama-Gutierrez Gabriela G   Banskota Samridhi S   Corona Guillermo Barreto GB   Chee Sora S   Chhetri Surya B SB   Cortez Martins Gabriel Conte GC   Danyko Cassidy C   Davis Carrie A CA   Farid Daniel D   Farrell Nina P NP   Gabdank Idan I   Gofin Yoel Y   Gorkin David U DU   Gu Mengting M   Hecht Vivian V   Hitz Benjamin C BC   Issner Robbyn R   Jiang Yunzhe Y   Kirsche Melanie M   Kong Xiangmeng X   Lam Bonita R BR   Li Shantao S   Li Bian B   Li Xiqi X   Lin Khine Zin KZ   Luo Ruibang R   Mackiewicz Mark M   Meng Ran R   Moore Jill E JE   Mudge Jonathan J   Nelson Nicholas N   Nusbaum Chad C   Popov Ioann I   Pratt Henry E HE   Qiu Yunjiang Y   Ramakrishnan Srividya S   Raymond Joe J   Salichos Leonidas L   Scavelli Alexandra A   Schreiber Jacob M JM   Sedlazeck Fritz J FJ   See Lei Hoon LH   Sherman Rachel M RM   Shi Xu X   Shi Minyi M   Sloan Cricket Alicia CA   Strattan J Seth JS   Tan Zhen Z   Tanaka Forrest Y FY   Vlasova Anna A   Wang Jun J   Werner Jonathan J   Williams Brian B   Xu Min M   Yan Chengfei C   Yu Lu L   Zaleski Christopher C   Zhang Jing J   Ardlie Kristin K   Cherry J Michael JM   Mendenhall Eric M EM   Noble William S WS   Weng Zhiping Z   Levine Morgan E ME   Dobin Alexander A   Wold Barbara B   Mortazavi Ali A   Ren Bing B   Gillis Jesse J   Myers Richard M RM   Snyder Michael P MP   Choudhary Jyoti J   Milosavljevic Aleksandar A   Schatz Michael C MC   Bernstein Bradley E BE   Guigó Roderic R   Gingeras Thomas R TR   Gerstein Mark M  

Cell 20230301 7

Understanding how genetic variants impact molecular phenotypes is a key goal of functional genomics, currently hindered by reliance on a single haploid reference genome. Here, we present the EN-TEx resource of 1,635 open-access datasets from four donors (∼30 tissues × ∼15 assays). The datasets are mapped to matched, diploid genomes with long-read phasing and structural variants, instantiating a catalog of >1 million allele-specific loci. These loci exhibit coordinated activity along haplotypes a  ...[more]

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