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Series GSE16256 Query DataSets for GSE16256
Status Public on Aug 03, 2009
Title UCSD Human Reference Epigenome Mapping Project
Project Roadmap Epigenomics
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
Summary The human embryonic stem cells (hESCs) are a unique model system for investigating the mechanisms of human development due to their ability to replicate indefinitely while retaining the capacity to differentiate into a host of functionally distinct cell types. In addition, these cells could be potentially used as therapeutic agents in regenerative medicine. Differentiation of hESCs involves selective activation or silencing of genes, a process controlled in part by the epigenetic state of the cell. In order to gain a better understanding of the epigenetic mechanisms regulating differentiation of hESCs, and produce general reference epigenome maps of the human cells, we propose to establish an Epigenome Center in San Diego. Our center will be focused on both undifferentiated hESC and four hESC-derived early embryonic cell lineages including extraembryonic endoderm, trophoblast, mesendoderm (a common precursor to mesodermal and endodermal lineages), and mesenchymal cells (a specific mesoderm derivative). We have developed and validated high throughput technologies for mapping the state of DNA methylation and chromatin modifications throughout the genome, and will use these methods to generate high-resolution maps of the reference epigenomes. Specifically, we will grow and differentiate hESCs into multiple lineages, and map DNA methylation sites using a newly developed technology that combines bisulfite conversion and whole genome shotgun sequencing. We will also determine the histone modification status in the genome by performing both ChlP-chip and ChlP-Seq analysis. We will develop advanced statistical and algorithmic solutions to facilitate high-throughput sequencing data analysis, and establish an informatics pipeline for collecting, storage, and distribution of epigenome maps. Finally, we will perform integrated data analysis to identify new epigenetic patterns in the genome that could provide insights in mechanisms of epigenetic regulation.

For data usage terms and conditions, please refer to:

Overall design UCSD Human Reference Epigenome Mapping Project - samples and experiments will continue to be added to this study over the course of the project.

EDACC Genboree Page:

Web link
Contributor(s) Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, Tonti-Filippini J, Nery JR, Lee L, Ye Z, Ngo Q, Edsall L, Antosiewicz-Bourget J, Stewart R, Ruotti V, Millar AH, Thomson JA, Ren B, Ecker JR
Citation(s) 19829295, 20452322, 20944595, 21289626, 26030523, 28637928, 23526891
BioProject PRJNA34535
Submission date May 27, 2009
Last update date Apr 16, 2020
Contact name UCSD AND SALK
Organization name University of California, San Diego
Street address Health Sciences Drive
City La Jolla
State/province CA
ZIP/Postal code 92092
Country USA
Platforms (6)
GPL9052 Illumina Genome Analyzer (Homo sapiens)
GPL9115 Illumina Genome Analyzer II (Homo sapiens)
GPL10999 Illumina Genome Analyzer IIx (Homo sapiens)
Samples (878)
GSM409307 Reference Epigenome: ChIP-Seq Analysis of H3K4me1 in hESC H1 (CDI-01) Cells; renlab.H3K4me1.CDI-01.01
GSM409308 Reference Epigenome: ChIP-Seq Analysis of H3K4me3 in hESC H1 (CDI-01) Cells; renlab.H3K4me3.CDI-01.01
GSM409312 Reference Epigenome: ChIP-Seq Analysis of H3K36me3 in hESC H1 (CDI-01) Cells; renlab.H3K36me3.CDI-01.01
SRA SRP000941

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Supplementary file Size Download File type/resource
GSE16256_RAW.tar 364.7 Gb (http)(custom) TAR (of BAM, BED, WIG)
SRA Run SelectorHelp
Raw data are available in SRA

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