Optimized approach for Ion Proton RNA sequencing reveals details of RNA splicing and editing features of the transcriptome.

ABSTRACT: RNA-sequencing (RNA-seq) has become the standard method for unbiased analysis of gene expression but also provides access to more complex transcriptome features, including alternative RNA splicing, RNA editing, and even detection of fusion transcripts formed through chromosomal translocations. However, differences in library methods can adversely affect the ability to recover these different types of transcriptome data. For example, some methods have bias for one end of transcripts or rely on low-efficiency steps that limit the complexity of the resulting library, making detection of rare transcripts less likely. We tested several commonly used methods of RNA-seq library preparation and found vast differences in the detection of advanced transcriptome features, such as alternatively splice

SUBMITTER: Brown RB 

PROVIDER: S-EPMC5411089 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature