BC Cancer Agency View Institution's Website 4 articles published in JoVE Genetics Generation of Native Chromatin Immunoprecipitation Sequencing Libraries for Nucleosome Density Analysis Alireza Lorzadeh1, Rodrigo Lopez Gutierrez1, Linda Jackson1, Michelle Moksa1, Martin Hirst1,2 1Department of Microbiology and Immunology, Michael Smith Laboratories Centre for High-Throughput Biology, University of British Columbia, 2Canada's Michael Smith Genome Science Center, BC Cancer Agency We present a modified native chromatin immunoprecipitation sequencing (ChIP-seq) methodology for the generation of sequence datasets suitable for a nucleosome density ChIP-seq analytical framework integrating micrococcal nuclease (MNase) accessibility with histone modification measurements. Biology DNA Extraction from Paraffin Embedded Material for Genetic and Epigenetic Analyses Larissa A. Pikor*1,2, Katey S. S. Enfield*1,2, Heryet Cameron3, Wan L. Lam1,2,4 1Department of Integrative Oncology, BC Cancer Research Centre, 2Interdisciplinary Oncology Program, University of British Columbia - UBC, 3Photography/Video Production, Multi-Media Services, BC Cancer Agency, 4Department of Pathology and Laboratory Medicine, University of British Columbia - UBC This video demonstrates the protocol for DNA extraction from formalin-fixed paraffin-embedded material. This is a multi-day procedure in which tissue sections are deparaffinized with xylene, rehydrated with ethanol and treated with proteinase K to purify and isolate DNA for subsequent gene-specific or genome-wide analysis. Biology Methylated DNA Immunoprecipitation Kelsie L. Thu*1,2, Emily A. Vucic*1,3, Jennifer Y. Kennett1,3, Cameron Heryet5, Carolyn J. Brown5, Wan L. Lam1,2,3, Ian M. Wilson1,3 1Department of Cancer Genetics and Developmental Biology, BC Cancer Research Centre, 2Interdisciplinary Oncology Program, University of British Columbia - UBC, 3Department of Pathology and Laboratory Medicine, University of British Columbia - UBC, 4Photography/Video Production, Multi-Media Services, BC Cancer Agency, 5Department of Medical Genetics, Life Sciences Institute,, University of British Columbia - UBC This video demonstrates the protocol for methylated DNA immunoprecipitation (MeDIP). MeDIP is a two day procedure that selectively extracts methylated DNA fragments from a genomic DNA sample using antibodies with specificity for 5 -methylcytosine (anti-5 mC). Biology Technical Demonstration of Whole Genome Array Comparative Genomic Hybridization Jennifer Y. Kennett1, Spencer K. Watson1, Heather Saprunoff2, Cameron Heryet3, Wan L. Lam1 1Department of Cancer Genetics, BC Cancer Research Centre, 2Deeley Research Centre, BC Cancer Agency, 3Photography/Video Production, Multi-Media Services, BC Cancer Agency This video is a technical demonstration of the hybridization protocol for whole genome tiling path array CGH, which scans the entire human genome using only 25-100 ng of DNA that can be isolated from a variety of sources, including archival formalin fixed material.