Epigenetics Core

University Of California Los Angeles, Los Angeles CA

Investigators

Linked publications & trials

Abstract

The Epigenetics Core (Core C) provides genome-wide DMA methylation, histone modification, and chromatin immunoprecipitation (ChIP) services, along with targeted gene region analysis and validation, to support the Program Projects. The Epigenetics Core provides direct linkage of services to the Administrative Core A, hESC Core B, Computational/Bioinformatics Core D and also to essential existing UCLA cores, including the Gene Expression Core Facility (S Nelson). The Epigenetics Core is strongly supported by Agilent Technologies (for array platforms, probe technologies, and analytical tool development and adoption) and by key consultants that support Core services, including C Plass and T Huang (DMA methylation), M Grunstein and S Kurdistani (histone modification), and H Cedar (ChIP). Core C will provide genome-wide or targeted detection and validation for altered patterns of DNA methylation in hESCs and derivative differentiated cells from the hESC Core B and from Program Projects 1-3. Core C provides ChIP procedures, probe manufacture, array hybridizations, data collection, and analysis through transfer of data to Computational/ Bioinformatics Core D. The Epigenetics Core will distribute information and protocols and help train personnel (as needed) in each of the Program Projects and Cores and will have a limited but important role in technology development, focusing mainly on reducing cell number inputs for array ChlP-chip technologies with Core users and assessing/incorporating advances in epigenetic modification detection as they become available through the general scientific community and in conjunction with Agilent Technologies. Access to the Solexa 1G high throughput sequencing system for advanced ChlP-chip analysis is through the UCLA Gene Expression Core Facility (S Nelson). As an essential comparative service to the Program Project and to the hESC community as a whole, Epigenetics Core C will provide baseline measurements of global DNA methylation, pan-acetylated histone H3 and H4, and di- and tri-methylated histones, epigenetic markings that reflect active or silenced gene expression, for optimally grown low-passage federally-approved hESC lines UC 01 (HSF-1), UC 06 (HSF-6), WA01 (H1), and Wa09 (H9) for comparative analysis. Expression profiling for these 4 federally-approved lines (already published or to be performed in the existing UCLA Gene Expression Core Facility) will provide a link between epigenetic signatures and effects on hESC gene expression. This information will be made available in a publicly accessible portion of the Program Project Website, with data entry and manipulation password protected.