Overview of services: The Epigenetics Core provides genome-wide DNA methylation, histone modification, and chromatin immunoprecipitation (ChIP) services, along with targeted gene region analysis and validation, to support wide range of projects within the UCLA IDDRC. Depending on the need of the users, the Core provides training and distributes information and protocols related to Core services. Data analysis is coordinated by the services of Core B1, Neurogenomics and Bioinformatics Core, under the direction of Dr. Geschwind. b. Staffing The director of the Core is Dr. Yi Sun. She has extensive experience on epigenetic analysis of neural stem cells, human embryonic stem cells and induced pluripotent stem (IPS) cells. She provides training and instructions in epigenetic analyses when necessary. An Assistant Researcher, Dr. Weihong Ge, is the day-today supervisor of the Epigenetics Core. She has considerable experience in all aspects of epigenetic analyses of the Core, as well as in running instrumentations specific to the Core. Dr. Sun devotes 5% of her time for directing the Core. Weihong Ge devotes 30% of her time towards Core activities and 30% of her salary is requested. c. Resources The Epigenetics Core is located in the 5th floor of the NRB (Room 555) as part of the Sun laboratory, and the Sequenom MassArray equipment is shared with the Southern California Genotyping Consortium located in Gonda (Goldschmied) Neuroscience and Genetics Research Center. The Core is centrally located between several neuroscience research centers (e.g., Gonda, MacDonald Research Laboratories (MRL) and Semel Institute for Neuroscience and Human Behavior). The Core has the following dedicated hardware and software for various genomic and epigenomic analyses (i.e., ChlP-chip for genome-wide location analysis of transcription factors and histone modifications, MeDIP-chip for DNA methylation profiling, whole genome gene expression profiling, array CGH for whole genome copy number variation profiling, and sequence capture for genome enrichment) in the NRB 5th floor space: Roche/NimbleGen hybridization system (4-bay model), NimbleScan software (version 2.5) and a dedicated computer running 64-bit Windows OS (with 8-GB RAM). All the sample preparations take place in the Core's NRB space. The Sequenom MassARRAY is located in the Gonda building and is used for running the reactions. Subsequently, data analysis is performed at the dedicated workstation within the Core. The workstation is set aside for at least 20 hours per week for member use, and IDDRC members have access to the workstation for additional data analysis when necessary. The workstation is loaded with appropriate software for the analysis of collected data through the Core. In addition, the Core has access to software in Dr. Geschwind's workstation in Core B1 (e.g., commercial programs such as Imagene and GeneSpring, and shareware such as Bio-Conductor, which are integrated into Dr. Geschwind laboratory and the IDDRC Neurogenomics and Bioinformatics Core B1). The interplay between the two Cores generate an environment in which standard, yet sophisticated epigenetic, genomic and statistical analyses can be performed by IDDRC members with the expertise of the Core personnel. Furthermore, the data obtained from the Core are stored in a way that it enables IDDRC users to share their data and perform analyses across different platforms.
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