| Autor: |
Nelson DC; Biotechnology Center and Biochemistry Department, University of Wisconsin, 425 Henry Mall, Madison, WI 53706, USA. msussman@wisc.edu, Wohlbach DJ, Rodesch MJ, Stolc V, Sussman MR, Samanta MP |
| Jazyk: |
angličtina |
| Zdroj: |
FEBS letters [FEBS Lett] 2007 Jul 24; Vol. 581 (18), pp. 3363-70. Date of Electronic Publication: 2007 Jun 26. |
| DOI: |
10.1016/j.febslet.2007.06.033 |
| Abstrakt: |
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 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. |
| Databáze: |
MEDLINE |
| Externí odkaz: |
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