The International Human Epigenomics Consortium (IHEC) has established an Assay Standards and Quality Control Working Group (Chaired by CEEHRC Network Leader Martin Hirst) to define the assays required for three distinct classes of reference epigenome, and to define standardized protocols and quality control metrics for each assay. The Working Group's recommendations are intended to provide a framework for the definition of reference epigenomes to be included within the International Human Epigenome Consortium. These recommendations are minimal standards based on current knowledge of the elements contributing to epigenomic regulation in human cells and the current state of epigenomic mapping technologies, and are reviewed and updated annually.
Standard Operating Procedures
As an additional resource, the specific epigenomics protocols used at the BC Cancer Agency Genome Sciences Centre are listed below. The linked documents represent the latest versions of all SOPs as of April 2017; if you require a different version of any of our SOPs, please contact us.
Sample preparation, nucleic acid extraction and QC
Whole genome sequencing (WGS)
Whole genome bisulfite sequencing (WGBS)
Chromatin immunoprecipitation sequencing (ChIP-Seq)
Validation and QC of ChIP-Seq reagents
Antibody Validation Data
Antibodies used for ChIP-Seq at the BC Cancer Agency Genome Sciences Centre are validated using the MODifiedTM Histone Peptide Array from Active Motif; ChIP and subsequent qPCR on genomic regions annotated as enriched or depleted for the histone modification in question; and Western blotting using whole cell extracts to test non-histone affinities.SOPs for all validation protocols are available above.
Validation data for each antibody lot used at our centre are available here (PDF) - last update April 10, 2017. Information about the antibodies used to generate specific ChIP-Seq libraries is available in the corresponding metadata files.
Data Analysis Methods
Index of all data analysis methods used.