Based on a normalized EST library generated from various tissues of an A. formosa x A. pubescens F2 population [20], a single channel oliognucleotide microarray platform representing more than 17,000 Aquilegia unigenes has been developed.
Our previous study employed a cDNA microarray platform representing about one-third of the genes in Drosophila.
In this study, we have examined data correspondence and discrepancy between MPSS and one-dye microarray platforms, representing sequencing-based and hybridization-based technologies, respectively.
Whole-genome gene expression (WGE) analyses through well-defined oligonucleotide microarray platforms represent a powerful tool for the molecular characterization of biological process.
Given the significant methodological differences between microarray and MPSS analysis, the fact that more than 65% of our MPSS differential data set showed concordance with expression profiling obtained by several different microarray platforms, represents a good overlap compared with other examples of sequence versus array data [ 41].
This custom microarray 4X44K platform represented almost all known genes in the mouse genome and their resulting transcripts in over 41000 60-mer oligonucleotide probe features.
Notably, these data sets were analyzed by different microarray platforms and represent patient materials of different stage, differentiation, ethnicity, age, and sex.
Although the microarray platform we used represented 25,030 non-redundant genes, we analyzed only those genes (N = 18,544) whose expression was determined with sufficient accuracy and whose transcription start sites (TSS) were known (see Methods for further detail).
This number has been considered sufficient by others to achieve over 90% coverage of the transcriptome, with as high or higher sensitivity than short oligonucleotide probe microarrays [ 33]. 16,220 of the 17,070 genes represented in every microarray platform could be detected through DGE.
Each platform represents one stage of enlightenment.
