Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Record number 449437
Title Consistent Errors in First Strand cDNA Due to Random Hexamer Mispriming
Author(s) Gurp, T.P. van; McIntyre, L.M.; Verhoeven, K.J.F.
Source PLoS One 8 (2013)12. - ISSN 1932-6203 - 4 p.
DOI http://dx.doi.org/10.1371/journal.pone.0085583
Department(s) Laboratory of Nematology
EPS
Publication type Refereed Article in a scientific journal
Publication year 2013
Keyword(s) dna-sequence differences - human transcriptome - widespread rna - discovery - biases
Abstract Priming of random hexamers in cDNA synthesis is known to show sequence bias, but in addition it has been suggested recently that mismatches in random hexamer priming could be a cause of mismatches between the original RNA fragment and observed sequence reads. To explore random hexamer mispriming as a potential source of these errors, we analyzed two independently generated RNA-seq datasets of synthetic ERCC spikes for which the reference is known. First strand cDNA synthesized by random hexamer priming on RNA showed consistent position and nucleotide-specific mismatch errors in the first seven nucleotides. The mismatch errors found in both datasets are consistent in distribution and thermodynamically stable mismatches are more common. This strongly indicates that RNA-DNA mispriming of specific random hexamers causes these errors. Due to their consistency and specificity, mispriming errors can have profound implications for downstream applications if not dealt with properly.
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