Imamachi N, Tani H, Mizutani R, Imamura K, Irie T, Suzuki Y, Akimitsu N. BRIC-seq: a genome-wide approach for determining RNA stability in mammalian cells.
Methods 2013;
67:55-63. [PMID:
23872059 DOI:
10.1016/j.ymeth.2013.07.014]
[Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2013] [Revised: 06/15/2013] [Accepted: 07/01/2013] [Indexed: 10/26/2022] Open
Abstract
We recently developed a novel transcriptome analysis method, termed 5'-bromo-uridine (BrU) immunoprecipitation chase-deep sequencing analysis (BRIC-seq). BRIC-seq enables the determination of genome-wide RNA stability by chasing chronological decreases of BrU-labeled RNAs under physiologically undisturbed conditions. The RNA half-life of each transcript is calculated from the decreasing number of BrU-labeled RNA sequence tags measured by deep sequencing of BrU-labeled RNAs. Here, we describe a detailed protocol and provide tips for BRIC-seq, followed by computational analysis.
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