Simultaneous genotyping, gene expression measurement, and detection of allele-specific expression

ABSTRACT: By hybridizing mRNA to oligonucleotide arrays and searching for probes that are outliers in their probe set, we identify and genotype polymorhisms in two strains of yeast (BY, isogenic to S288C, and RM, a wild vineyard strain) and segregants from a cross between the two strains. We then use this mRNA based genotyping approach to study allele-specific expression in diploid hybrids from a cross between BY and RM. A 1:1 mixture of BY and RM parental mRNA is created and hybridized to arrays as a control in these allele-specific expression experiments. The S. cerevisiae strains BY4716, an S288C derivative, and RM11-1a, a haploid Bb32(3) derivative, are described elsewhere (Brem et al. 2002, Yvert et al. 2003). We grew cultures to 10e7 cells/mL in shake flasks at 175 rpm at 300 C in synthetic C medium. We followed the standard Affymetrix protocol for preparation of RNA samples and for hybridization of the samples to Affymetrix YGS98 expression arrays. In total, three cultures of the BY strain, three cultures of the RM strain, one culture of each of the two haploid segregants and the two diploid segregants hybrids, three cultures of the BY-BY hybrid, three cultures of the RM-RM hybrid, and six cultures of the BY-RM hybrid were analyzed. Values calculated using the method described by Zhang et al. (Nat Biotechnol. 21, 818-821). The results are part of Ronald et al. (2005) describing a novel use of oligonucleotide expression arrays to perform genotyping. This method requires the use of individual probe signals, rather than the overall probeset value as is produced by analysis programs such as MAS or RMA.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE1975 | GEO | 2004/11/16

SECONDARY ACCESSION(S): PRJNA90919

REPOSITORIES: GEO