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- Study Description
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Important Links and Information
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- Instructions for requestors
- Data Use Certification (DUC) Agreement
- Talking Glossary of Genetic Terms
Working cooperatively with other Mapping Centers and the Data Coordination Center (EDACC) funded by this Roadmap mechanism we have comprehensively mapped the epigenomes of select human cells with significant relevance to complex human disease. Our effort has been focused on cells relevant to human health and complex disease including cells from the blood, brain, breast, skin, male germ cells, extraembryonic tissues and trophoblast, and U.S. Government-approved lines of human embryonic stem cells. We have incorporated high quality, homogeneous cells from males and females, and two predominant racial groups, and biological replicates of each cell type. The resulting comprehensive maps include up to 6 histone modifications selected for their opposing roles in regulating active and inactive chromatin (H3K4me1, H3K4me3, H3K9me3, H3K9ac, H3K27ac, H3K27me3, H3K36me3), DNA methylation, miRNA and gene expression, and for select cases whole genome shotgun sequence. Our cell and data production pipeline incorporates verification and data validation with independent methods, and operates under a model motivated by increased data production and decrease cost. Our group in conjunction with the other REMC teams, the EDACC, ENCODE, Epigenetics of Human Health and Disease centers and the NIH Roadmap program are developing methods, tools and reference epigenome maps for the research community that will make the promise of epigenetics in understand and treating human complex disease a reality. Our reference epigenomes will enable new disciplines including human population epigenetics, comparative epigenomics, neuroepigenetics, and therapeutic epigenetics for tissue regeneration and reversal of disease.
- Study Weblinks:
- Study Design:
- Control Set
- Study Type:
- Control Set
- Total number of consented subjects: 50
- Subject Sample Telemetry Report (SSTR)
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- Authorized Access
- Publicly Available Data
- Link to other NCBI resources related to this study
- Molecular Data
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Type Source Platform Number of Oligos/SNPs SNP Batch Id Comment ChIP-Sequencing Illumina HiSeq 2000 N/A N/A ChIP-Sequencing Illumina Genome Analyzer II N/A N/A ChIP-Sequencing Illumina Genome Analyzer IIX N/A N/A Whole Genome Sequencing Illumina HiSeq 2000 N/A N/A Messenger RNA Sequencing Illumina HiSeq 2000 N/A N/A Messenger RNA Sequencing Illumina Genome Analyzer II N/A N/A Messenger RNA Sequencing Illumina Genome Analyzer IIX N/A N/A Whole Genome Bisulfite Sequencing Illumina HiSeq 2000 N/A N/A MicroRNA Sequencing Illumina HiSeq 2000 N/A N/A MicroRNA Sequencing Illumina Genome Analyzer IIX N/A N/A Methylated DNA Immunoprecipitation Sequencing Illumina HiSeq 2000 N/A N/A Methylated DNA Immunoprecipitation Sequencing Illumina Genome Analyzer II N/A N/A Methylated DNA Immunoprecipitation Sequencing Illumina Genome Analyzer IIX N/A N/A Methylation-Sensitive Restriction Enzyme Sequencing Illumina HiSeq 2000 N/A N/A Methylation-Sensitive Restriction Enzyme Sequencing Illumina Genome Analyzer II N/A N/A Methylation-Sensitive Restriction Enzyme Sequencing Illumina Genome Analyzer IIX N/A N/A - Study History
Biospecimens profiled within this project were derived from normal, disease-free adult and fetal tissues and cells.
- Selected Publications
- Diseases/Traits Related to Study (MeSH terms)
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- Primary Phenotype: Neoplasms
- Authorized Data Access Requests
- Study Attribution
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Principal Investigator
- Costello, Joseph, F. PhD. Department of Neurological Surgery, University California San Francisco, San Francisco, CA, USA.
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Co-Investigator
- Hirst, Martin. PhD. Canada's Michael Smith Genome Science Center, BC Cancer Agency, Department of Microbiology and Immunology, Centre for High-Throughput Biology, University of British Columbia, Vancouver, BC, Canada.
- Wang, Ting. PhD. Washington University, Department of Genetics, St. Louis, MO, USA.
- Marra, Marco, A. PhD. Canada's Michael Smith Genome Science Center, BC Cancer Agency, and Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.
- Farnham, Peggy J. PhD. Department of Biochemistry and Molecular Biology, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA.
- Fisher, Susan. PhD. Department of Cell and Tissue Biology, University California San Francisco, San Francisco, CA, USA.
- Haussler, David. PhD. Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA, USA.
- Jones, Steven JM. PhD. Canada's Michael Smith Genome Science Center, BC Cancer Agency, Canada.
- McManus, Michael. PhD. Department of Microbiology and Immunology, University California San Francisco, San Francisco, CA, USA.
- Tlsty, Thea. PhD. Department of Neurological Surgery, Pathology and Microbiology and Immunology, University California San Francisco, San Francisco, CA, USA.
- Weiss, Arthur. M.D. PhD. Howard Hughes Medical Institute and Department of Rheumatology, University California San Francisco, San Francisco, CA, USA.
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Funding Source
- 5U01ES017154-02. US National Institutes of Health (NIH) Roadmap Epigenomics Program, National Institutes of Health, MD, Bethesda, USA.
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Principal Investigator