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Series GSE16368 Query DataSets for GSE16368
Status Public on Aug 03, 2009
Title UCSF-UBC Human Reference Epigenome Mapping Project
Project Roadmap Epigenomics
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Summary The epigenome is the dynamic interface between our changing environment and the static genome, and understanding it is a goal of immense importance to human health. We will map reference cell epigenomes of the brain, breast, blood and approved embryonic stem cells, inclusive of males and females and different racial groups. This cooperative work will transform our understanding of the short and long-lasting consequences of environment impact on human health and disease.

We are working cooperatively with other Mapping Centers and the Data Coordination Center (EDACC) to comprehensively map epigenomes of select human cells with significant relevance to complex human disease. Our group, consisting of scientists at UCSF, UC Davis, UCSC and the British Columbia Genome Sciences Centre will focus on cells relevant to human health and complex disease including cells from the blood, brain, breast and U.S. Government-approved lines of human embryonic stem cells. We will incorporate high quality, homogeneous cells from males and females, and two predominant racial groups, and biological replicates of each cell type. Production of comprehensive maps will include 6 histone modifications selected for their opposing roles in regulating active and inactive chromatin, DNA methylation and miRNA and gene expression. This epigenetic data, along with genetic and expression data will be integrated using advanced informatics to address fundamental roles of epigenetics in differentiation, maintenance of cell-type identity and gene expression. Our cell and data production pipeline will incorporate verification and data validation with independent methods, and will operate under a model motivated by increased data production and decrease cost. We summarize the analysis capacity of our instruments and our explicit strategy for data sharing of our proposed REMC-generated resources including biological specimens, protocols, data, software tools and intellectual resources. We envision that our group in conjunction with the other REMC teams, the EDACC, ENCODE, future EHHD (Epigenetics of Human Health and Disease) centers and the NIH Roadmap program will develop 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.

Contributor: BCCA Genome Sciences Centre

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For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
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Overall design UCSF-UBC Human Reference Epigenome Mapping Project - samples, experiments and processed data files will continue to be added to this study as the project proceeds.

EDACC Genboree Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSF-UBC%2FSTUDY%2FEDACC.822
Web link http://www.ncbi.nlm.nih.gov/geo/roadmap/epigenomics/
 
Citation(s) 20944595, 25690954
BioProject PRJNA34535
Submission date Jun 01, 2009
Last update date May 15, 2019
Contact name UCSF-UBC CENTER
Organization name UCSF-UBC
Street address UCSF-UBC
City San Francisco
State/province CA
ZIP/Postal code 94143
Country USA
 
Platforms (3)
GPL9115 Illumina Genome Analyzer II (Homo sapiens)
GPL10999 Illumina Genome Analyzer IIx (Homo sapiens)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (529)
GSM410807 H3K9ac ChIP-Seq analysis of H1 embryonic stem cell line (HS0995)
GSM410808 H3K4me3 ChIP-Seq analysis of H1 embryonic stem cell line (HS0996)
GSM428286 MRE-Seq analysis of H1 embryonic stem cell line (HS1052)
Relations
SRA SRP046944

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE16368_RAW.tar 363.9 Gb (http)(custom) TAR (of BAM, BED, TAB, WIG)
SRA Run SelectorHelp
Raw data are available in SRA
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