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Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Molecular Medicine. Uppsala University, Science for Life Laboratory, SciLifeLab.
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2013 (English)In: Nature Biotechnology, ISSN 1087-0156, E-ISSN 1546-1696, Vol. 31, no 11, 1015-1022 p.Article in journal (Refereed) Published
Abstract [en]

RNA sequencing is an increasingly popular technology for genome-wide analysis of transcript sequence and abundance. However, understanding of the sources of technical and interlaboratory variation is still limited. To address this, the GEUVADIS consortium sequenced mRNAs and small RNAs of lymphoblastoid cell lines of 465 individuals in seven sequencing centers, with a large number of replicates. The variation between laboratories appeared to be considerably smaller than the already limited biological variation. Laboratory effects were mainly seen in differences in insert size and GC content and could be adequately corrected for. In small-RNA sequencing, the microRNA (miRNA) content differed widely between samples owing to competitive sequencing of rRNA fragments. This did not affect relative quantification of miRNAs. We conclude that distributing RNA sequencing among different laboratories is feasible, given proper standardization and randomization procedures. We provide a set of quality measures and guidelines for assessing technical biases in RNA-seq data.

Place, publisher, year, edition, pages
2013. Vol. 31, no 11, 1015-1022 p.
National Category
Genetics Bioinformatics and Systems Biology Medical Genetics
Research subject
Genetics
Identifiers
URN: urn:nbn:se:uu:diva-207893DOI: 10.1038/nbt.2702ISI: 000326921200023PubMedID: 24037425OAI: oai:DiVA.org:uu-207893DiVA: diva2:650224
Funder
EU, FP7, Seventh Framework Programme
Available from: 2013-09-20 Created: 2013-09-20 Last updated: 2017-12-06Bibliographically approved

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Almlöf, JonasKarlberg, OlofBrännvall, MathiasSyvänen, Ann-Christine

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