A Comparison of microarray and MPSS Technology Platforms for Expression Analysis of Arabidopsis. Arabidopsis thaliana

A comparison of microarray and MPSS technologies can help to establish the metrics for data comparisons across these technology platforms and determine some of the factors affecting the measurement of mRNA abundances using different platforms. Here, different Treatments/Conditions based on different Arabidopsis tissues were used for three different platforms include MPSS, Affymetrix and Agilent. Keywords: MPSS, Affymetrix, Agilent Overall design: For the comparison, 11 different samples were used: Callus, Inforescence, Leaf, Root, Silique, Afamous Inflorescence, Ap1-10 Inflorescence, Ap3-6 Inflorescence, Sup/Ap1 Inflorescence, Leaves SA 4 hr and Leaves SA 52 hr. For details about samples, see Meyers Lab (http://mpss.udel.edu/at). All RNA samples were created in Meyers Lab. MPSS experiments were performed in Meyers Lab. Affymetrix experiments were performed in St. Clair Lab (http://stclairlab.ucdavis.edu/). Agilent experiments were performed by Sean J Coughlan from Agilent (http://www.agilent.com/). Two replicates for each samples were used in Affymetrix platform except Silique sample. Two replicates for each samples were used in Agilent platform.