BC Cancer Agency

4 ARTICLES PUBLISHED IN JoVE

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.

Biology

Methylated DNA Immunoprecipitation

Kelsie L. Thu^*1,2, Emily A. Vucic^*1,3, Jennifer Y. Kennett^1,3, Cameron Heryet⁵, Carolyn J. Brown⁵, Wan L. Lam^1,2,3, Ian M. Wilson^1,3

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

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. Lam^1,2,4

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.

Genetics

Generation of Native Chromatin Immunoprecipitation Sequencing Libraries for Nucleosome Density Analysis

Alireza Lorzadeh¹, Rodrigo Lopez Gutierrez¹, Linda Jackson¹, Michelle Moksa¹, Martin Hirst^1,2

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.