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Published on: July 12, 2012
Protocol for high-throughput DNA methylation profiling in rat tissues using automated reduced representation
Venugopalan D Nair1, Hanna Pincas1, Mary Anne S Amper1
1Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
STAR Protocols
|May 1, 2024
Summary
We developed a high-throughput, automated protocol for reduced representation bisulfite sequencing (RRBS) to efficiently measure DNA methylation (DNAme) in rat tissues, overcoming common assay limitations.
Area of Science:
- Genomics
- Epigenetics
- Molecular Biology
Background:
- Reduced representation bisulfite sequencing (RRBS) is a sensitive method for DNA methylation analysis.
- Traditional RRBS protocols can be lengthy and susceptible to batch variations.
Purpose of the Study:
- To present a high-throughput, automated RRBS protocol for DNA methylation profiling.
- To optimize RRBS workflow from DNA extraction to data processing for rat tissues.
Main Methods:
- DNA extraction from frozen rat tissues.
- Automated RRBS library preparation, quality control, and sequencing.
- Optimized bioinformatics pipeline for sequencing data analysis.
Main Results:
- Successful application of the protocol for DNA methylation profiling across multiple rat tissues.
- Demonstration of a streamlined and efficient RRBS workflow.
Conclusions:
- The developed automated RRBS protocol enhances throughput and reduces batch effects.
- This method provides a robust approach for large-scale DNA methylation studies in rat models.
