Unknown,Transcriptomics,Genomics,Proteomics

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RNA-seq of coding RNA of 19 human tissues from fetuses with congenital defects (NIH Roadmap Epigenomics Mapping Consortium)


ABSTRACT: The NIH Roadmap Epigenomics Mapping Consortium aims to produce a public resource of epigenomic maps for stem cells and primary ex vivo tissues selected to represent the normal counterparts of tissues and organ systems frequently involved in human disease. This data set was submitted by University of Washington as part of GSE18927 ( http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18927 ) / SRP001371 at NCBI Gene Expression Omnibus and Sequence Read Archive respectively. The ArrayExpress record here contains only RNA-seq meta-data for the 53 human fetal samples covering 19 different tissues/organs from 23 fetuses. You can find out more about WashU's contribution to this project here: http://egg2.wustl.edu/roadmap/web_portal/index.html. The full set of NIH Epigenome Project data (not limited to RNA-seq) can be found here: http://www.ncbi.nlm.nih.gov/geo/roadmap/epigenomics

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Homo sapiens

SUBMITTER: Northwest Reference Epigenome Mapping Project NIH Roadmap Epigenomics Mapping Consortium 

PROVIDER: E-MTAB-3871 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Integrative analysis of 111 reference human epigenomes.

Kundaje Anshul A   Meuleman Wouter W   Ernst Jason J   Bilenky Misha M   Yen Angela A   Heravi-Moussavi Alireza A   Kheradpour Pouya P   Zhang Zhizhuo Z   Wang Jianrong J   Ziller Michael J MJ   Amin Viren V   Whitaker John W JW   Schultz Matthew D MD   Ward Lucas D LD   Sarkar Abhishek A   Quon Gerald G   Sandstrom Richard S RS   Eaton Matthew L ML   Wu Yi-Chieh YC   Pfenning Andreas R AR   Wang Xinchen X   Claussnitzer Melina M   Liu Yaping Y   Coarfa Cristian C   Harris R Alan RA   Shoresh Noam N   Epstein Charles B CB   Gjoneska Elizabeta E   Leung Danny D   Xie Wei W   Hawkins R David RD   Lister Ryan R   Hong Chibo C   Gascard Philippe P   Mungall Andrew J AJ   Moore Richard R   Chuah Eric E   Tam Angela A   Canfield Theresa K TK   Hansen R Scott RS   Kaul Rajinder R   Sabo Peter J PJ   Bansal Mukul S MS   Carles Annaick A   Dixon Jesse R JR   Farh Kai-How KH   Feizi Soheil S   Karlic Rosa R   Kim Ah-Ram AR   Kulkarni Ashwinikumar A   Li Daofeng D   Lowdon Rebecca R   Elliott GiNell G   Mercer Tim R TR   Neph Shane J SJ   Onuchic Vitor V   Polak Paz P   Rajagopal Nisha N   Ray Pradipta P   Sallari Richard C RC   Siebenthall Kyle T KT   Sinnott-Armstrong Nicholas A NA   Stevens Michael M   Thurman Robert E RE   Wu Jie J   Zhang Bo B   Zhou Xin X   Beaudet Arthur E AE   Boyer Laurie A LA   De Jager Philip L PL   Farnham Peggy J PJ   Fisher Susan J SJ   Haussler David D   Jones Steven J M SJ   Li Wei W   Marra Marco A MA   McManus Michael T MT   Sunyaev Shamil S   Thomson James A JA   Tlsty Thea D TD   Tsai Li-Huei LH   Wang Wei W   Waterland Robert A RA   Zhang Michael Q MQ   Chadwick Lisa H LH   Bernstein Bradley E BE   Costello Joseph F JF   Ecker Joseph R JR   Hirst Martin M   Meissner Alexander A   Milosavljevic Aleksandar A   Ren Bing B   Stamatoyannopoulos John A JA   Wang Ting T   Kellis Manolis M  

Nature 20150201 7539


The reference human genome sequence set the stage for studies of genetic variation and its association with human disease, but epigenomic studies lack a similar reference. To address this need, the NIH Roadmap Epigenomics Consortium generated the largest collection so far of human epigenomes for primary cells and tissues. Here we describe the integrative analysis of 111 reference human epigenomes generated as part of the programme, profiled for histone modification patterns, DNA accessibility, D  ...[more]

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