Optimization of the Omni-ATAC protocol to chromatin accessibility profiling in snap-frozen rat adipose and muscle tissues.
Optimization of the Omni-ATAC protocol to chromatin accessibility profiling in snap-frozen rat adipose and muscle tissues.
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DOI：
10.1016/j.mex.2022.101681
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发表时间：
2022
期刊：
影响因子：
1.9
通讯作者：
Sealfon, Stuart C.
中科院分区：
文献类型：
--
作者：
Nair, Venugopalan D.;Vasoya, Mital;Nair, Vishnu;Smith, Gregory R.;Pincas, Hanna;Ge, Yongchao;Douglas, Collin M.;Esser, Karyn A.;Sealfon, Stuart C.
关键词：
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. ATAC-seq is a fast and sensitive method for the epigenomic profiling of open chromatin and for mapping of transcription factor binding sites. Despite the development of the Omni-ATAC protocol for the profiling of chromatin accessibility in frozen tissues, 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.
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