High-Resolution RT-PCR Analysis of Alternative Barley Transcripts

Craig G. Simpson (Lead / Corresponding author), John Fuller, Paulo Rapazote-Flores, Claus Dieter Mayer, Cristiane P. G. Calixto, Linda Milne, Pete E. Hedley, Clare Booth, Robbie Waugh, John W. S. Brown

Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)peer-review

1 Citation (Scopus)
167 Downloads (Pure)


Assembly of the barley genome and extensive use of RNA-seq has resulted in an abundance of gene expression data and the recognition of wide-scale production of alternatively spliced transcripts. Here, we describe in detail a high-resolution reverse transcription-PCR based panel (HR RT-PCR) that confirms the accuracy of alternatively spliced transcripts from RNA-seq and allows quantification of changes in the proportion of splice isoforms between different experimental conditions, time points, tissues, genotypes, ecotypes, and treatments. By validating a selection of barley genes, use of the panel gives confidence or otherwise to the genome-wide global changes in alternatively spliced transcripts reported by RNA-seq. This simple assay can readily be applied to perform detailed transcript isoform analysis for any gene in any species.

Original languageEnglish
Title of host publicationBarley
Subtitle of host publicationMethods and Protocols
EditorsWendy A. Harwood
Place of PublicationNew York
PublisherHumana Press
Number of pages13
ISBN (Electronic)9781493989447
ISBN (Print)9781493989423
Publication statusPublished - 2019

Publication series

NameMethods in Molecular Biology
ISSN (Print)1064-3745


  • Alternative splicing
  • RNA-seq

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics


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