title: A high-performance, small-scale microarray for expression profiling of many samples in Arabidopsis-pathogen studies.
abstract: Studies of the behavior of biological systems often require monitoring of the expression of many genes in a large number of samples. While whole-genome arrays provide high-quality gene-expression profiles, their high cost generally limits the number of samples that can be studied. Although inexpensive small-scale arrays representing genes of interest could be used for many applications, it is challenging to obtain accurate measurements with conventional small-scale microarrays. We have developed a small-scale microarray system that yields highly accurate and reproducible expression measurements. This was achieved by implementing a stable gene-based quantile normalization method for array-to-array normalization, and a probe-printing design that allows use of a statistical model to correct for effects of print tips and uneven hybridization. The array measures expression values in a single sample, rather than ratios between two samples. This allows accurate comparisons among many samples. The array typically yielded correlation coefficients higher than 0.99 between technically duplicated samples. Accuracy was demonstrated by a correlation coefficient of 0.88 between expression ratios determined from this array and an Affymetrix GeneChip, by quantitative RT-PCR, and by spiking known amounts of specific RNAs into the RNA samples used for profiling. The array was used to compare the responses of wild-type, rps2 and ndr1 mutant plants to infection by a Pseudomonas syringae strain expressing avrRpt2. The results suggest that ndr1 affects a defense-signaling pathway(s) in addition to the RPS2-dependent pathway, and indicate that the microarray is a powerful tool for systems analyses of the Arabidopsis disease-signaling network.
authors.affiliation: Department of Plant Biology, Microbial and Plant Genomics Institute, University of Minnesota, 1500 Gortner Avenue, St Paul, MN 55108, USA.
authors.forename: Masanao
authors.initials: M
authors.lastname: Sato
authors.forename: Raka M
authors.initials: RM
authors.lastname: Mitra
authors.forename: John
authors.initials: J
authors.lastname: Coller
authors.forename: Dong
authors.initials: D
authors.lastname: Wang
authors.forename: Natalie W
authors.initials: NW
authors.lastname: Spivey
authors.forename: Julia
authors.initials: J
authors.lastname: Dewdney
authors.forename: Carine
authors.initials: C
authors.lastname: Denoux
authors.forename: Jane
authors.initials: J
authors.lastname: Glazebrook
authors.forename: Fumiaki
authors.initials: F
authors.lastname: Katagiri
mesh_terms: D017360:Arabidopsis / Q000235:genetics / Q000276:immunology / Q000378:metabolism*; D029681:Arabidopsis Proteins / Q000502:physiology; D020869:Gene Expression Profiling / Q000295:instrumentation* / Q000379:methods; D008962:Models, Theoretical; D008969:Molecular Sequence Data; D021141:Nucleic Acid Amplification Techniques; D020411:Oligonucleotide Array Sequence Analysis / Q000295:instrumentation*; D010935:Plant Diseases; D015203:Reproducibility of Results; D015398:Signal Transduction / Q000502:physiology; D014157:Transcription Factors / Q000502:physiology
chemical_list: D029681:Arabidopsis Proteins; C109369:NDR1 protein, Arabidopsis; C089426:RPS2 protein, Arabidopsis; D014157:Transcription Factors