Time-course microarray study of Cryptococcus neoformans var. neoformans spore germination

To identify the genome-wide transcriptional changes that occur throughout germination of C. neoformans spores, we conducted a time-course microarray experiment spanning six timepoints to generate a temporal expression pattern for each known gene. Spores were placed in rich medium and allowed to germinate for 10 hours, when they start to replicate as yeast. Each time point was flash frozen in liquid nitrogen and RNA was harvested for each time point at the same time. Microarray hybridizations were conducted in a reference pool design, where each time point was mixed together in equal amounts to make a reference pool sample. Then each time point was hybrdized against the reference pool. Characterization of the genes and pathways that are regulated during germination of this ubiquitous fungal pathogen will allow us to better understand how infectious spores resume vegetative growth, a process that likely is critical for interaction between C. neoformans and a host. The experiment spanned six time points of germination: 0 hours (dormant spores), 2 hours, 4 hours, 6 hours, 8 hours and 10 hours. Hybridizations were conducted in a reference pool design, with a mixture of each sample serving as the reference pool. This design results in 6 experimental comparisons: 0 Hr vs Reference pool (REF), 2 Hhr vs REF, 4 Hr vs REF, 6 Hr vs REF, 8 Hr vs Ref, and 10 Hr vs REF. Each comparison consistent of duplicate hybridizations with dye swaps. Arrays contain duplicate genomes, resulting in eight-fold coverage within each comparison. (total of 24 hybridizations)