Evaluation of alternative RNA labeling protocols for transcript profiling with Arabidopsis AGRONOMICS1 tiling arrays

Plant Methods

Lars Hennig²  Wilhelm Gruissem³  Hubert Rehrauer³  Andrea Patrignani³  Marlen Müller¹ 

[1] Department of Biology, Plant Biotechnology, ETH Zurich, Zurich, Switzerland;Department of Plant Biology and Forest Genetics, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, PO-Box 7080, SE-75007, Uppsala, Sweden;Functional Genomics Center Zurich, ETH and University of Zurich, CH-8057, Zurich, Switzerland

关键词: RNA labeling;    Tiling array;    AGRONOMICS1;    Microarray;    Arabidopsis;    Transcript profiling;   

Others  :  822491
DOI  :  10.1186/1746-4811-8-18

 received in 2012-01-31, accepted in 2012-06-13,  发布年份 2012

【 摘 要 】

Microarrays are routine tools for transcript profiling, and genomic tiling arrays such as the Arabidopsis AGRONOMICS1 arrays have been found to be highly suitable for such experiments because changes in genome annotation can be easily integrated at the data analysis level. In a transcript profiling experiment, RNA labeling is a critical step, most often initiated by oligo-dT-primed reverse transcription. Although this has been found to be a robust and reliable method, very long transcripts or non-polyadenylated transcripts might be labeled inefficiently. In this study, we first provide data handling methods to analyze AGRONOMICS1 tiling microarrays based on the TAIR10 genome annotation. Second, we describe methods to easily quantify antisense transcripts on such tiling arrays. Third, we test a random-primed RNA labeling method, and find that on AGRONOMICS1 arrays this method has similar general performance as the conventional oligo-dT-primed method. In contrast to the latter, however, the former works considerably better for long transcripts and for non-polyadenylated transcripts such as found in mitochondria and plastids. We propose that researchers interested in organelle function use the random-primed method to unleash the full potential of genomic tiling arrays.

【 授权许可】

   
2012 Müller et al.; licensee BioMed Central Ltd.

【 图 表 】

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