RNA polymerase II ChIP-seq-a powerful and highly affordable method for studying fungal genomics and physiology.
作者信息
Tan Kaeling, Wong Koon Ho
机构信息
Faculty of Health Sciences, University of Macau, Avenida da Universidade, Taipa, Macau SAR, China.
Genomics and Bioinformatics core, Faculty of Health Sciences, University of Macau, Avenida da Universidade, Taipa, Macau SAR, China.
出版信息
Biophys Rev. 2019 Feb;11(1):79-82. doi: 10.1007/s12551-018-00497-9. Epub 2019 Jan 9.
Abstract
摘要
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2
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3
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7
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