Protocols and Standards

IHEC Guidelines

The International Human Epigenomics Consortium (IHEC) has established an Assay Standards Working Group 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 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 will be reviewed and updated annually.

As an additional resource, the specific protocols used at the BC Cancer Agency Genome Sciences Centre are listed below.

General

SLX-PET protocol for Illumina sample prep
Guidelines for preparing templates from gDNA, cDNA, or ChIP DNA for Illumina paired-end sequencing.
Last updated: November 30, 2012

DNA

DNA sonication using Sonic Dismembrator 550
Prior to Illumina library construction or other applications.
Last updated: June 6, 2011

Operation and maintenance of the Covaris E-series
For shearing DNA to the appropriate size range for library construction.
Last updated: February 27, 2012

RNA

Purification of polyA+ mRNA and mRNA(-) Flow-through total RNA fractions using a MultiMACS 96 separation unit
For transcriptome and microRNA library construction, respectively.
Last updated: November 30, 2012

Strand-specific cDNA Synthesis, 96-well plate format
Prior to Illumina library construction.
Last updated: May 18, 2012

Strand-specific RNA-Seq Illumina library construction, 96-well plate format
Last updated: July 31, 2012

miRNA Illumina library construction, 96-well plate format
Last updated: December 3, 2012

Chromatin

Validation data for ChIP-Seq antibodies(pdf)
(Validation data by Antibody)

Crosslinking adherent cell lines
Last updated: December 11, 2012

Crosslinking frozen cell pellets or small pieces of tissue
To be performed immediately prior to a ChIP experiment.
Last updated: December 11, 2012

Chromatin Immunoprecipitation (ChIP) on crosslinked cells
Last updated: September 26, 2012

Data Analysis Methods

Index of all data analysis methods used.