IHEC Guidelines
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 2018; if you require a different version of any of our SOPs, please contact us.
- Wet Lab
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- Sample preparation, nucleic acid extraction and QC
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- Transfer and Cutting of Tissue Samples
- Snap Freezing Protocol For Tissue
- Homogenization of Tissue using Tissue Lyser LT
- Harvesting Cell Lines for DNA/RNA Extraction and ChIP
- DNA/RNA Extraction with AllPrep (DNA) and mirVana (total RNA with small RNA) Isolation Kits
- Quantifying DNA samples using the Qubit Fluorometer
- Automated DNA Quantification using the dsDNA Quant-iT High Sensitivity Assay Kit and VICTOR3V
- Operation and Maintenance of the Agilent 2100 Bioanalyzer for DNA samples
- Operation and Maintenance of the Agilent 2100 Bioanalyzer for RNA Samples
- Operation and maintenance of the Caliper LabChip GX for DNA Samples using the High Sensitivity Assay
- Operation and Maintenance of the LabChipGX for RNA samples using the HT RNA Assay
- Whole genome sequencing (WGS)
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- DNA Sonication using Sonic Dismembrator 550
- Operation of the Covaris LE220
- 96-well PCR free Library Construction for Illumina Sequencing
- 96-well PCR Free Library Construction on NIMBUS for Illumina Sequencing
- 96-well PCR-enriched Library Construction for Illumina Sequencing
- Nimbus-assisted 96-well PCR-enriched Library Construction for Illumina Sequencing
- 96-well Genomic ~350bp-450bp insert Illumina Library Construction
- Whole genome bisulfite sequencing (WGBS)
- RNA-Seq
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- Magnetic bead-based mRNA isolation
- Plate-based rRNA depletion Version 1
- Plate-Based rRNA Depletion (RBD2.0)
- Purification of polyA+ mRNA and mRNA(-) Flow-Through Total RNA using MultiMACS 96 Separation Unit
- Purification of polyA+ mRNA and mRNA(-) Flow-Through Total RNA using Nimbus-assisted MultiMACS 96 Separation Unit
- Strand Specific 96 Well cDNA Synthesis
- 96-well Plate-based Strand-specific cDNA Synthesis using Maxima H Minus
- 96-well Plate-based Strand-specific cDNA Synthesis using Maxima H Minus on Hamilton NIMBUS
- Strand Specific 96-well Library Construction for Illumina Sequencing
- Nimbus-assisted 96-well PCR-enriched Library Construction for Illumina Sequencing
- MicroRNA-Seq
- Chromatin immunoprecipitation sequencing (ChIP-Seq)
- Validation and QC of ChIP-Seq reagents
- Other assays
