6 protocols
AccessionNameType
P-GSE45383-1
bioassay_data_transformation
ID_REF = VALUE = RMA normalized probe expression values
P-GSE45383-6
feature_extraction
Raw data were RMA normalized using Nimblescan software. Probe expression values were used to determine fold-change and filtered to significantly induced and repressed probe lists (p≤0.01 as determined by student’s t- test). Gene lists were generated based on the occurrence of at least two probes for a particular gene present exclusively in induced or repressed probe lists.
P-GSE45383-5
image_aquisition
Performed according to the manufacturer’s protocol
P-GSE45383-4
hybridization
Performed according to the manufacturer’s protocol
P-GSE45383-3
labeling
Performed according to the manufacturer’s protocol
P-GSE45383-2
nucleic_acid_extraction
RNA extraction and purification were performed as described (Bonawitz et al., 2008) from wild-type DBY2006 and rph1Δ cultures grown for 24 hours after addition of 50 μM menadione or ethanol. RNA quality bioanalysis, cDNA synthesis, and hybridization to a Roche/NimbleGen 12x135K array were performed in collaboration with the Yale University W.M. Keck Foundation Biotechnology Resource Laboratory according to the manufacturer’s protocol. Two independent biological replicates were prepared for each sample, and hybridization was performed in duplicate to generate technical replicates.