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Epigenetics Core

Epigenetics Core. Subhashinee Samudra K. Wijeratne , Ph.D. Dept. of Nutrition and Health Sciences, UNL. Processes in Epigenetics The study of heritable changes in gene expression or cellular phenotype caused by mechanisms other than changes in the underlying DNA sequence.

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Epigenetics Core

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  1. Epigenetics Core SubhashineeSamudra K. Wijeratne, Ph.D. Dept. of Nutrition and Health Sciences, UNL

  2. Processes in Epigenetics • The study of heritable changes in gene expression or cellular phenotype caused by mechanisms other than changes in the underlying DNA sequence. • Chromatin remodeling • DNA methylation • Histone modifications • RNA interference

  3. EpigeneticsCore • Requirements for epigenetic studies • Personnel • Formal training in epigenetics study design • Laboratory techniques • Data analysis • Equipment • The Epigenetics Core will be the only facility in the State of Nebraska with in-depth capabilities and expertise with regard to the analysis of epigenetic marks.

  4. EpigeneticsCore Specific Aim 1 Renovate institutionally committed space on the University of Nebraska-Lincoln (UNL) campus to create a epigeneticscore research facility dedicated to serving the needs of Center and non-Center researchers.

  5. Core Location • Ruth LevertonHall, East Campus, UNL. • Approximately 800 sq.ft. • LevertonHall • Nutrition and Health Sciences. • NPOD administrative office. • Easy access. • Parking availability. • Funds • Alteration and renovation of the space. • Purchase and installation of fixed equipment. • Moveable/portable equipment.

  6. Epigenetics Core- Floor Plan

  7. EpigeneticsCore Specific Aim 2 Provide means by which NPOD project leaders and other Center members can discover new signaling mechanisms at a reasonable cost, while receiving valuable guidance regarding experimental design, data analysis, and data interpretation.

  8. EpigeneticsCore Specific Aim 3 Provide training for NPOD investigators and members of their laboratories on experimental procedure and techniques.

  9. Services • Consulting: Study designs

  10. Services Sample Analysis • DNA methylation. • Histone modification marks. • Sample preparation for subsequent second-generation sequencing. • Mapping of epigenetic marks and transcription factor binding sites in mammalian chromatin.

  11. Services DataAnalysis • Consulting services ondata analysis and interpretation. • Antibody testing. Comprehensive service package: Including cell culture, antibody testing, consulting on experimental designs, sample analysis, biostatistical analysis (large data sets), and staff training for user laboratories.

  12. Services • Training sessions • Free training sessions to members affiliated with the NPOD • Enhance the research expertise in members’ laboratories. • To develop an epigenetics workforce in Nebraska. • Investigators fromother institutions: • Develop more formalized training sessions (and charge a nominal fee).

  13. Services • Priority Junior Investigators > Other center members > External users • FeeStructure • Each JI : $2,000 credit /year of project funding. • Remaining credit: • Carry forward to the next year. • Transfer to another center member. • Once the credits are exhausted JIs will be required to pay a fee that covers the cost of supplies, etc. • The same fee will be paid by other center members and external users.

  14. Immediate Users NPOD Project Leaders • Regis Moreau (Anti-lipemicMechanism of (R)-alpha-lipoic Acid) • Dmitri Fomenko(Selenoproteinsand Selenium-dependent Redox Signaling Alter Diabetes Risk) • Jennifer Wood (Abnormalities in Epigenetic Regulation of Skeletal and Cardiac Muscle Differentiation by Maternal Obesity) • SaraswathiViswanathan (The Lipid-lowering Effects of ω-3 Fatty Acids are Mediated by Pregnane X Receptor and Constitutive Androstane Receptor Signaling) ChIP, Realtime PCR and Sequencing MicroChIP with Realtime PCR DNA methylation with Realtime PCR and cloning Antibody validation

  15. Other Users • Other NPOD Users • Dr. Donald Becker, Dr. Cyrus Desouza, Dr. Robert Lewis, • Dr. Etsuko Moriyama, Dr. Janos Zempleni, Dr. John Davis, • Dr. Angela Pannier, Dr. Andrea Cupp, Dr. Samodha Fernando, • Dr. Vicki Schlegel, Dr. XinBi • Other Center members with research programs in epigenetics • Dr. Patrick Dussault and Dr. Mark Wilson • Non-Center members at UNL and UNMC • Dr. ZoyaAvramova, Dr. Gloria Borgstahl, Dr. HeribertoCerutti, Dr. Judy Christman, Dr. Michael Fromm, Dr. Steve Ladunga, • Dr. Yuri Lyubchenko • Users from other Institutes/collaborators • Dr. Emily Ho, Dr. Ji-Young Lee, Dr. Don Mock, • Dr. DonatoRomagnolo, Dr. John West

  16. Expected Outcomes of the Epigenetics Core • Increase the competiveness of University of Nebraska researchers in securing external funding. • Create an environment conducive to the development of highly talented junior investigator transitioning to independent status. • Support the development of important new collaborations among Center members and beyond, and help in the development of a national workforce.

  17. Support for the Epigenetics Core • Initial • The Center. • In the long-term • Self-sustained through service fees paid • by Center members and non-members alike. • The Epigenetics Core will be the only facility in NE that offers a comprehensive service, including cell culture, antibody testing, experimental design assistance, sample analysis, biostatisticalanalysis, and laboratory staff training.

  18. Core Personnel • Core Director : SubhashineeSamudraK. Wijeratne, Ph.D. • Five years of experience in epigenetics and cell biology. • Formal training in food science and nutrition. • Serves as main consultant for projects. • Responsible for budget, and staff supervision. • Co-Director: Sridhar Malkaram, Ph.D. • Four years experience in epigenetics and • computational biology. • Formal training in molecular and computational biology. • Study design and data analysis (bioinformatics) consultant.

  19. Core Personnel • Laboratory Technician: Mengna Xia, M.S • Formal training in animal genetics, breeding, and reproduction. • Two years of experience in epigenetics research. • Analyzing epigenetic marks in mammalian chromatin and testing antibody specificities.

  20. Equipment Centrifuges and microcentrifuges Digital Sonicator Thermocycler Cell Incubator Refrigerated Shaking Incubator Nanodrop Spectrophotometer Freezers (-80C and -20C) Real Time PCR

  21. Equipment Western Blot units Agarose Gel Electrophoresis Units Cold Storage Unit LiCOR Imaging System Balances Thermal Mixer and Tube Rotator Inverted Microscope Sterile Cabinet (48'')

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