Optimization of the Omni-ATAC protocol to chromatin accessibility profiling in snap-frozen rat adipose and muscle tissues
Venugopalan D. Nair,
Mital Vasoya,
Vishnu Nair,
Gregory R. Smith,
Hanna Pincas,
Yongchao Ge,
Collin M. Douglas,
Karyn A. Esser,
Stuart C. Sealfon
Affiliations
Venugopalan D. Nair
Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Corresponding author.
Mital Vasoya
Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
Vishnu Nair
Department of Computer Sciences, Columbia University, New York, NY 10027, USA
Gregory R. Smith
Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
Hanna Pincas
Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
Yongchao Ge
Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
Collin M. Douglas
Department of Physiology and Functional Genomics, University of Florida, Gainesville, FL 32610, USA
Karyn A. Esser
Department of Physiology and Functional Genomics, University of Florida, Gainesville, FL 32610, USA
Stuart C. Sealfon
Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
ATAC-seq is a fast and sensitive method for the epigenomic profiling of open chromatin and for mapping of transcription factor binding sites [1]. Despite the development of the Omni-ATAC protocol for the profiling of chromatin accessibility in frozen tissues [2], studies in adipose tissue have been restricted due to technical challenges including the high lipid content of adipocytes and reproducibility issues between replicates. Here, we provide a modified Omni-ATAC protocol that achieves high data reproducibility in various tissue types from rat, including adipose and muscle tissues [3]. • This protocol describes a methodology that enables chromatin accessibility profiling from snap-frozen rat adipose and muscle tissues. • The technique comprises an optimized bead-based tissue homogenization process that substitutes to Dounce homogenization, reduces variability in the experimental procedure, and is adaptable to various tissue types. • In comparison with the Omni-ATAC protocol, the method described here results in improved ATAC-seq data quality that complies with ENCODE quality standards.
