Format:
Online-Ressource
Content:
In most organisms, ribosomal RNA (rRNA) contributes to 〉85% of total RNA. Thus, to obtain useful information from RNA-sequencing (RNA-seq) analyses at reasonable sequencing depth, typically, mature polyadenylated transcripts are enriched or rRNA molecules are depleted. Targeted depletion of rRNA is particularly useful when studying transcripts lacking a poly(A) tail, such as some non-coding RNAs (ncRNAs), most bacterial RNAs and partially degraded or immature transcripts. While several commercially available kits allow effective rRNA depletion, their efficiency relies on a high degree of sequence homology between oligonucleotide probes and the target RNA. This restricts the use of such kits to a limited number of organisms with conserved rRNA sequences. In this study we describe the use of biotinylated oligos and streptavidin-coated paramagnetic beads for the efficient and specific depletion of trypanosomal rRNA. Our approach reduces the levels of the most abundant rRNA transcripts to less than 5% with minimal off-target effects. By adjusting the sequence of the oligonucleotide probes, our approach can be used to deplete rRNAs or other abundant transcripts independent of species. Thus, our protocol provides a useful alternative for rRNA removal where enrichment of polyadenylated transcripts is not an option and commercial kits for rRNA are not available.
In:
Datenlieferant: Open Access LMU (Ludwig-Maximilians-University Munich)
Language:
English
DOI:
10.1038/s41598-019-48692-2
URN:
urn:nbn:de:bvb:19-epub-81589-9
URL:
https://doi.org/10.1038/s41598-019-48692-2
URL:
https://nbn-resolving.org/urn:nbn:de:bvb:19-epub-81589-9
URL:
https://epub.ub.uni-muenchen.de/81589/1/s41598-019-48692-2.pdf
URL:
https://epub.ub.uni-muenchen.de/81589/
Bookmarklink