کد مقاله | کد نشریه | سال انتشار | مقاله انگلیسی | نسخه تمام متن |
---|---|---|---|---|
10872432 | 1074141 | 2007 | 8 صفحه PDF | دانلود رایگان |
عنوان انگلیسی مقاله ISI
Identification of an in vitro transcription-based artifact affecting oligonucleotide microarrays
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کلمات کلیدی
موضوعات مرتبط
علوم زیستی و بیوفناوری
علوم کشاورزی و بیولوژیک
دانش گیاه شناسی
پیش نمایش صفحه اول مقاله

چکیده انگلیسی
This study identified the widely used T7 in vitro transcription system as a major source of artifact in the tiling array data from nine 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 5â² 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.
ناشر
Database: Elsevier - ScienceDirect (ساینس دایرکت)
Journal: FEBS Letters - Volume 581, Issue 18, 24 July 2007, Pages 3363-3370
Journal: FEBS Letters - Volume 581, Issue 18, 24 July 2007, Pages 3363-3370
نویسندگان
David C. Nelson, Dana J. Wohlbach, Matthew J. Rodesch, Viktor Stolc, Michael R. Sussman, Manoj P. Samanta,