ncRNAseq: simple modifications to RNA-seq library preparation allow recovery and analysis of mid-sized non-coding RNAs.
Published version
Peer-reviewed
Repository URI
Repository DOI
Type
Article
Change log
Authors
Minshall, Nicola https://orcid.org/0000-0002-8350-4903
Chernukhin, Igor https://orcid.org/0000-0002-4411-1218
Carroll, Jason S https://orcid.org/0000-0003-3643-0080
Git, Anna https://orcid.org/0000-0003-0973-9138
Abstract
Despite their abundance, mid-sized RNAs (30-300 nt) have not been extensively studied by high-throughput sequencing, mostly due to selective loss in library preparation. The authors propose simple and inexpensive modifications to the Illumina TruSeq protocol (ncRNAseq), allowing the capture and sequencing of mid-sized non-coding RNAs without detriment to the coverage of coding mRNAs. This protocol is coupled with a two-step alignment: a pre-alignment to a curated non-coding genome, passing only the non-mapping reads to a standard genomic alignment. ncRNAseq correctly assigns the highest read-numbers to established abundant non-coding RNAs and correctly identifies cytosolic and nuclear enrichment of known non-coding RNAs in two cell lines.
Description
Keywords
5′ coverage, high-throughput sequencing, next-generation sequencing, non-coding RNA, size-selection, Gene Library, High-Throughput Nucleotide Sequencing, RNA, Untranslated, RNA-Seq, Sequence Analysis, RNA
Journal Title
Biotechniques
Conference Name
Journal ISSN
0736-6205
1940-9818
1940-9818
Volume Title
72
Publisher
Future Science Ltd
Publisher DOI
Sponsorship
Breast Cancer Now (2016NovPR816)