Protocol for high-throughput DNA methylation profiling in rat tissues using automated reduced representation bisulfite sequencing

Venugopalan D. Nair; Hanna Pincas; Mary Anne S. Amper; Yongchao Ge; Mital Vasoya; Archana Natarajan Raja; Martin J. Walsh; Stuart C. Sealfon

doi:10.1016/j.xpro.2024.103007

Protocol for high-throughput DNA methylation profiling in rat tissues using automated reduced representation bisulfite sequencing

Venugopalan D. Nair, Hanna Pincas, Mary Anne S. Amper, Yongchao Ge, Mital Vasoya, Archana Natarajan Raja, Martin J. Walsh, Stuart C. Sealfon

Research output: Contribution to journal › Article › peer-review

Abstract

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

Original language	English
Article number	103007
Journal	STAR Protocols
Volume	5
Issue number	2
DOIs	https://doi.org/10.1016/j.xpro.2024.103007
State	Published - 21 Jun 2024

Keywords

Genomics
High-Throughput Screening
Molecular Biology

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10.1016/j.xpro.2024.103007

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title = "Protocol for high-throughput DNA methylation profiling in rat tissues using automated reduced representation bisulfite sequencing",

abstract = "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",

keywords = "Genomics, High-Throughput Screening, Molecular Biology",

author = "Nair, {Venugopalan D.} and Hanna Pincas and Amper, {Mary Anne S.} and Yongchao Ge and Mital Vasoya and Raja, {Archana Natarajan} and Walsh, {Martin J.} and Sealfon, {Stuart C.}",

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month = jun,

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doi = "10.1016/j.xpro.2024.103007",

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T1 - Protocol for high-throughput DNA methylation profiling in rat tissues using automated reduced representation bisulfite sequencing

AU - Nair, Venugopalan D.

AU - Pincas, Hanna

AU - Amper, Mary Anne S.

AU - Ge, Yongchao

AU - Vasoya, Mital

AU - Raja, Archana Natarajan

AU - Walsh, Martin J.

AU - Sealfon, Stuart C.

PY - 2024/6/21

Y1 - 2024/6/21

N2 - 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

AB - 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

KW - Genomics

KW - High-Throughput Screening

KW - Molecular Biology

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U2 - 10.1016/j.xpro.2024.103007

DO - 10.1016/j.xpro.2024.103007

M3 - Article

AN - SCOPUS:85191419754

SN - 2666-1667

VL - 5

JO - STAR Protocols

JF - STAR Protocols

IS - 2

M1 - 103007

ER -

Protocol for high-throughput DNA methylation profiling in rat tissues using automated reduced representation bisulfite sequencing

Abstract

Keywords

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