normalization data transformation protocol
The data were normalized with Robust Multi-array Analysis(RMA) algorithm using Affymetrix default analysis settings ID_REF = VALUE = Log2 scaled expression values normalized by the RMA algorithm
array scanning protocol
The microarrays were subsequently scanned using the Affymetrix GeneChip Scanner 3000 7G
Total RNA samples were hybridized to the microarrays. The microarrays were washed several times to eliminate non-specific hybridization.
Biotinylated cRNA were prepared according to the standard Affymetrix protocol
M2 and M2 nsf1∆ strains were cultured over-night in YPD broth to obtain a sufficient number of cells. 4 L of Riesling grape must purchased from Kamil Juices (http://www.kamiljuices.com/) in 2010 was sterile filtered into 1L bottles and left over-night at 18 °C in incubator. The following day, the M2 and M2 nsf1∆ cultures were briefly washed in sterile dH2O and the cell number calculated using a hemocytometer. Each 1L of Riesling grape must was inoculated to a final 2.6x10^6cells/mL that corresponded to OD600 of 0.1. After inoculation, the 1L flasks were incubated at 18°C without shaking. 100 mL samples were taken at 3 time points: 24h after inoculation, 20% and 85% glucose fermentented. The isolated cells were used for total RNA extraction for microarray analysis. The overall experimental setup consisted of 2 stains and 3 sample time points.
nucleic acid extraction protocol
Phenol:Chloroform:Isoamyl Alcohol (25:24:1) pH 6.8 standard RNA extraction with NaCl precipitation protocol followed by the Qiagen™ RNeasy silica based column RNA cleanup
sample treatment protocol
No additional treatments were applied to the M2 and M2 and M2 nsf1∆ strains