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Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution
Published on: February 24, 2015
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Protocol for generating high-quality genome-scale DNA methylation sequencing data from human cancer biospecimens
Euan J Rodger1, Peter A Stockwell1, Suzan Almomani1
1Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand.
STAR Protocols
|November 11, 2023
Summary
This study details a protocol for high-quality DNA methylation sequencing across diverse cancer samples. The method enables comprehensive methylome profiling for cancer research and other diseases.
Area of Science:
- Epigenetics
- Genomics
- Cancer Biology
Background:
- Aberrant DNA methylation is a hallmark of cancer.
- Understanding cancer epigenetics requires robust genome-scale methylation data.
Purpose of the Study:
- To present a standardized protocol for generating high-quality genome-scale DNA methylation sequencing data.
- To enable comprehensive methylome profiling across various human cancer biospecimens.
Main Methods:
- DNA extraction optimization for different tissue types.
- Reduced representation bisulfite sequencing (RRBS) methodology.
- Bioinformatic pipeline for data processing, quality control, and analysis.
Main Results:
- Successful generation of high-quality DNA methylation data from cell lines, fresh-frozen, and FFPE tissues.
- A comprehensive protocol applicable to diverse sample types and organisms.
- Established framework for downstream data integration and analysis.
Conclusions:
- The presented protocol facilitates robust methylome profiling in cancer.
- This method is adaptable for studying other human diseases and non-human organisms.
- Standardized epigenomic data generation is crucial for advancing cancer research.
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