The T7-Primer Is a Source of Experimental Bias and Introduces Variability between Microarray Platforms

Eberwine(-like) amplification of mRNA adds distinct 6-10 bp nucleotide stretches to the 5' end of amplified RNA transcripts. Analysis of over six thousand microarrays reveals that probes containing motifs complementary to these stretches are associated with aberrantly high signals up to a hundr...

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Vydáno v:	PloS one Ročník 3; číslo 4; s. e1980
Hlavní autoři:	Kerkhoven, Ron M., Sie, Daoud, Nieuwland, Marja, Heimerikx, Mike, De Ronde, Jorma, Brugman, Wim, Velds, Arno
Médium:	Journal Article
Jazyk:	angličtina
Vydáno:	United States Public Library of Science 23.04.2008 Public Library of Science (PLoS)
Témata:	Aberration Acids Antisense RNA Bacteriophage T7 - metabolism Base Sequence Bias Binding Sites Breast cancer Datasets DNA microarrays DNA Primers - genetics DNA Primers - metabolism DNA probes DNA, Intergenic - genetics DNA-Directed RNA Polymerases - metabolism Enzymes Gene expression Gene Expression Regulation Gene sequencing Genetics and Genomics/Bioinformatics Genetics and Genomics/Gene Expression Genomes Humans Hybridization Messenger RNA Molecular Biology/Bioinformatics Molecular Sequence Data Oligonucleotide Array Sequence Analysis Operon - genetics Platforms Probes Quality control Ribonucleic acid RNA RNA, Messenger - genetics RNA, Messenger - metabolism RNA, Viral - genetics Studies Viral Proteins - metabolism Netherlands
ISSN:	1932-6203, 1932-6203
On-line přístup:	Získat plný text
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Shrnutí:	Eberwine(-like) amplification of mRNA adds distinct 6-10 bp nucleotide stretches to the 5' end of amplified RNA transcripts. Analysis of over six thousand microarrays reveals that probes containing motifs complementary to these stretches are associated with aberrantly high signals up to a hundred fold the signal observed in unaffected probes. This is not observed when total RNA is used as target source. Different T7 primer sequences are used in different laboratories and platforms and consequently different T7 primer bias is observed in different datasets. This will hamper efforts to compare data sets across platforms.
Bibliografie:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 14 content type line 23 Conceived and designed the experiments: RK. Performed the experiments: DS MN MH WB. Analyzed the data: DS Jd AV. Contributed reagents/materials/analysis tools: DS MN MH Jd WB AV. Wrote the paper: RK DS Jd AV.
ISSN:	1932-6203 1932-6203
DOI:	10.1371/journal.pone.0001980