Analysis of oligp hybridization properties by high-resolution tiling microarrays in rice

摘要

Rice genome sequencing and computational annotation provide a static map for understanding this model of Gramineae species. With the development of in situ oligonucleotide synthesis technology, tiling-path microarrays have become a dynamic and efficient way for monitoring large-scale transcriptional activities and detecting novel transcribed elements missed by software. Unlike conventional cDNA or oligonucleotide arrays, tiling-path platforms employ the full extent of oligos covering given genomic regions, and thus offer excellent experimental conditions in which to assay the properties of oligos in terms of their specificity and efficiency of hybridization to their corresponding targets. Here, we report a tiling-path microarray analysis of a 1-Mb region (10 to 11 Mb) in japonica rice chromosome 10, which was tiled by a 36-mer oligo set at a resolution of 5 bp. Our analysis focused on three major factors of oligo hybridization properties, including GC content, melting temperature (Tm), and the repetitiveness of oligo sequences.