Improved TGIRT-seq methods for comprehensive transcriptome profiling with decreased adapter dimer formation and bias correction.

ABSTRACT: Thermostable group II intron reverse transcriptases (TGIRTs) with high fidelity and processivity have been used for a variety of RNA sequencing (RNA-seq) applications, including comprehensive profiling of whole-cell, exosomal, and human plasma RNAs; quantitative tRNA-seq based on the ability of TGIRT enzymes to give full-length reads of tRNAs and other structured small ncRNAs; high-throughput mapping of post-transcriptional modifications; and RNA structure mapping. Here, we improved TGIRT-seq methods for comprehensive transcriptome profiling by rationally designing RNA-seq adapters that minimize adapter dimer formation. Additionally, we developed biochemical and computational methods for remediating 5'- and 3'-end biases, the latter based on a random forest regression model that provides i

SUBMITTER: Xu H 

PROVIDER: S-EPMC6538698 | biostudies-literature | 2019 May

REPOSITORIES: biostudies-literature