Protocol for high-throughput DNA methylation profiling in rat tissues using automated reduced representation bisulfite sequencing.
| Autor: | Nair VD; Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA. Electronic address: venugopalan.nair@mountsinai.org., Pincas H; Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA., Amper MAS; Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA., Ge Y; Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA., Vasoya M; Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA., Raja AN; Department of Medicine, Stanford School of Medicine, Stanford, CA 94305, USA., Walsh MJ; Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA., Sealfon SC; Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA. Electronic address: stuart.sealfon@mssm.edu. |
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| Jazyk: | angličtina |
| Zdroj: | STAR protocols [STAR Protoc] 2024 Jun 21; Vol. 5 (2), pp. 103007. Date of Electronic Publication: 2024 Apr 30. |
| DOI: | 10.1016/j.xpro.2024.103007 |
| Abstrakt: | Although reduced representation bisulfite sequencing (RRBS) measures DNA methylation (DNAme) across CpG-rich genomic regions with high sensitivity, the assay can be time-consuming and prone to batch effects. Here, we present a high-throughput, automated RRBS protocol starting with DNA extraction from frozen rat tissues. We describe steps for RRBS library preparation, library quality control, and sequencing. We also detail an optimized pipeline for sequencing data processing. This protocol has been applied successfully to DNAme profiling across multiple rat tissues. For complete details on the use and execution of this protocol, please refer to Nair et al. 1 . Competing Interests: Declaration of interests The authors declare no competing interests. (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.) |
| Databáze: | MEDLINE |
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