Pseudo-Seq: Genome-Wide Detection of Pseudouridine Modifications in RNA.RNA molecules contain a variety of chemically diverse, posttranscriptionally modified bases.  Here, we present Pseudo-seq, a technique that allows the identification of sites of pseudouridylation genome-wide with single-nucleotide resolution.  In this chapter, we provide a detailed description of Pseudo-seq.  We include protocols for RNA isolation from Saccharomyces cerevisiae, Pseudo-seq library preparation, and data analysis, including descriptions of processing and mapping of sequencing reads, computational identification of sites of pseudouridylation, and assignment of sites to specific pseudouridine synthases. 
Pseudo-seq
Pseudo-Seq: Genome-Wide Detection of Pseudouridine Modifications in RNA.RNA molecules contain a variety of chemically diverse, posttranscriptionally modified bases.  Here, we present Pseudo-seq, a technique that allows the identification of sites of pseudouridylation genome-wide with single-nucleotide resolution.  In this chapter, we provide a detailed description of Pseudo-seq.  We include protocols for RNA isolation from Saccharomyces cerevisiae, Pseudo-seq library preparation, and data analysis, including descriptions of processing and mapping of sequencing reads, computational identification of sites of pseudouridylation, and assignment of sites to specific pseudouridine synthases. 
Pseudo-seq