Bioinformatics Pipeline to Analyze lncRNA Arrays

Katia Todoerti, Domenica Ronchetti, Martina Manzoni, Elisa Taiana, Antonino Neri, Luca Agnelli

Research output: Contribution to journalArticlepeer-review

Abstract

Despite the fact that next-generation sequencing approaches, in particular RNA sequencing, provide deep genome-wide expression data that allow both careful annotations/mapping of long noncoding RNA (lncRNA) molecules and de-novo sequencing, lncRNA expression studies by microarray is a still cost-effective procedure that could allow to have a landscape of the most characterized lncRNA species. However, microarray design does not always correctly address the overlap between coding and noncoding samples to discriminate between the original transcript source. In order to overcome this issue, in this chapter we present a bioinformatics pipeline that enables accurate annotation of GeneChip® microarrays, to date the most commonly adopted among the commercial solutions. Overall, this approach holds two main advantages, a gain in specificity of transcript detection and the adaptability to the whole panel of GeneChip® arrays.

Original languageEnglish
Pages (from-to)45-53
Number of pages9
JournalMethods in molecular biology (Clifton, N.J.)
Volume2348
DOIs
Publication statusPublished - 2021

Keywords

  • lncRNA
  • Microarrays

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

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