Transcription profiling of Arabidopsis to assess spiking

ABSTRACT: Transcript profiling is crucial to study biological systems and various platforms have been implemented to survey mRNAs at the genome scale. We have assessed the characteristics of the CATMA microarray designed for Arabidopsis thaliana transcriptome analysis, and compared it with two commercial platforms from Agilent and Affymetrix. The CATMA array consists of gene-specific sequence tags of 150 to 500 base pairs, the Agilent (Arabidopsis 2) array of 60mer oligonucleotides, and the Affymetrix gene chip (ATH1) of 25mer oligonucleotide sets. We have matched each probe repertoire with the Arabidopsis genome annotation (TIGR release 5.0) and determined the correspondence between them. Array performance was analyzed by hybridization with labeled target derived from eight RNA samples made of shoot total RNA spiked with a calibrated series of 14 control transcripts. CATMA arrays showed the largest dynamic range extending over three to four logs. Agilent and Affymetrix arrays displayed a narrower range because signal saturation occurred for transcripts at concentrations beyond 1000 copies per cell. Sensitivity is comparable for all three platforms. For Affymetrix genechip data, the RMA software package outperformed MAS 5.0 for all investigated criteria, confirming that the information provided by the mismatch oligonucleotides has no added value analysis. In addition, taking advantage of replicates in our dataset we conducted a robust in statistical analysis of the platform propensity to yield false positive and negative differentially expressed genes, and all platforms gave satisfactory results. With adequate production and processing management, the CATMA array may offer a significant cost benefit to potential users.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Paul Van Hummelen 

PROVIDER: E-MEXP-197 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress