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Published on: September 16, 2019
ncRNAseq: simple modifications to RNA-seq library preparation allow recovery and analysis of mid-sized non-coding
Nicola Minshall1, Igor Chernukhin2, Jason S Carroll2
1Department of Biochemistry, University of Cambridge, Cambridge, UK.
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.
