6 protocols
AccessionType
bioassay_data_transformation
The normalization of the raw data for all probe sets was performed with the GeneChip Operating software from Affimetrix and the mask file for Yeast Genome 2.0 arrays for S. cerevisiae.
image_acquisition
The arrays were washed and stained in a GeneChip Scanner 3000 and the GeneChip Operating software from Affimetrix according to the instructions manual for Yeast genome 2.0 arrays.
(Parameters: Scanning hardware = GeneChip Scanner 3000 [Affymetrix], Scanning software = Scanning software)
labeling
250 microgram of total RNA was labelled with biotin using the GeneChip 3-IVT Express Kit Assay from Affimetrix according to the instructions manual
(Parameters: Amount of nucleic acid labeled = 250, Amplification = none, Mass unit = Micro gram)
nucleic_acid_extraction
Total RNA from frozen samples was extracted using Qiagen RNeasy Mini Kit (Yeast Protocol 1c (mechanical disruption).
(Parameters: Extracted product = total_RNA, Amplification = none)
grow
Yeast strains were grown in YNB medium supplemented with 0,4mM tryptophan, 0,2mM uracil and 2% glucose. For each strain two independent colonies were used. Overnight cultures were diluted into 30ml of fresh medium to an OD600 of 0.25 and grown to an OD600 of 1.0 at 30 degrees C while shaking.
(Parameters: start time = 6, time unit = hours, min temperature = 30, temperature unit = C, media = YNB + tryptophane + uracil)
hybridization
Hybridization was carried out according to the instructions manual of the GeneChip 3-IVT Express Kit from Affimetrix (Target Hybridization for Cartridge Arrays, 169 (mini)).
(Parameters: Chamber type = Affymetrix- GeneChip Hyb Oven 640, Quantity of label target used = 5, Mass unit = Micro gram, time = 16, Tiny time unit = hours, Volume = 80, Volume unit = Micro litre, temperature = 45)