Long Intergenic Noncoding RNA (lincRNA) Discovery from Non-Strand-Specific RNA-Seq Data

A A Golicz

doi:10.1007/978-1-0716-2067-0_24

Long Intergenic Noncoding RNA (lincRNA) Discovery from Non-Strand-Specific RNA-Seq Data

Methods Mol Biol. 2022:2443:465-482. doi: 10.1007/978-1-0716-2067-0_24.

Author

A A Golicz¹

Affiliation

¹ Department of Plant Breeding, Justus Liebig University Gießen, Gießen, Germany. Agnieszka.Golicz@agrar.uni-giessen.de.

PMID: 35037221
DOI: 10.1007/978-1-0716-2067-0_24

Abstract

Long noncoding RNAs (lncRNAs) are transcripts over 200 base pairs in length without discernible protein coding potential. Long intergenic noncoding RNAs (lincRNAs) constitute a subset of lncRNAs, which do not overlap protein coding genes. Here we describe a detailed pipeline for lincRNA discovery from publicly available non-stranded RNA-Seq datasets. The pipeline presented can be applied to any plant species for which RNA-Seq data and a reference genome sequence are available.

Keywords: Genome annotation; Long intergenic noncoding RNA; RNA-Seq; Transcriptome; lincRNA.

MeSH terms

Genome
RNA, Long Noncoding* / genetics
RNA, Long Noncoding* / metabolism
RNA-Seq
Transcriptome

Substances

RNA, Long Noncoding