Identification of an in vitro transcription-based artifact affecting oligonucleotide microarrays

David Nelson, D.J. Wohlbach, M.J. Rodesch, V. Stolc, M.R. Sussman, M.P. Samanta

Research output: Contribution to journalArticle

5 Citations (Scopus)

Abstract

This study identified the widely used T7 in vitro transcription system as a major source of artifact in the tiling array data fromnine eukaryotic genomes. The most affected probes contained a sequence motif complementary to the +1 to +9 initial transcribed sequence (ITS) of the T7-(dT)(24) primer. The abundance of 5' ITS cRNA fragments produced during target preparation was sufficient to drive undesirable hybridization. A new T7-(dT)24 primer with a modified ITS; was designed that shifts the artifactual motifs as predicted and reduces the effect of the artifact. A computational algorithm was generated to filter out the likely artifactual probes from existing whole-genome tiling array data and improve probe selection. Further studies of Arabidopsis thaliana were conducted using both T7-(dT)24 primers. While the artifact affected transcript discovery with tiling arrays, it showed only a minor impact on measurements of gene expression using commercially available 'gene-only' expression arrays. (c) 2007 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.
Original languageEnglish
Pages (from-to)3363-3370
JournalFEBS Letters
Volume581
DOIs
Publication statusPublished - 2007

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    Nelson, D., Wohlbach, D. J., Rodesch, M. J., Stolc, V., Sussman, M. R., & Samanta, M. P. (2007). Identification of an in vitro transcription-based artifact affecting oligonucleotide microarrays. FEBS Letters, 581, 3363-3370. https://doi.org/10.1016/j.febslet.2007.06.033