6 protocols
AccessionNameType
P-GSE46145-1
normalization data transformation protocol
Data procesing was performed according to [Pierce SE, Davis RW, Nislow C, Giaever G (2007) Genome-wide analysis of barcoded Saccharomyces cerevisiae gene-deletion mutants in pooled cultures. Nat Protocols 2: 2958-2974]. Perl scripts were downloaded from the supplementary web [Pierce, S.E. et al. A unique and universal molecular barcode array. Nat. Methods 3, 601-603 (2006)]. Data were normalized by quantile. Extracted data are in natural scale, but Ratios used for discussion in the associated manuscript are expressed in log2. ID_REF = VALUE = quantile normalized signal intensity
P-GSE46145-6
array scanning protocol
GeneChips were scanned at an emission wavelength of 560 nm using a GeneChip scanner (Affymetrix).
P-GSE46145-5
hybridization protocol
Reactions hybridized overnight to custom-built TAG4 microarrays (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to [Pierce SE, Davis RW, Nislow C, Giaever G (2007) Genome-wide analysis of barcoded Saccharomyces cerevisiae gene-deletion mutants in pooled cultures. Nat Protocols 2: 2958-2974]
P-GSE46145-4
labelling protocol
Amplification of the barcodes (uptags and downtags), with simoultaneous labelling using biotinilated primers was performed according to [Pierce SE, Davis RW, Nislow C, Giaever G (2007) Genome-wide analysis of barcoded Saccharomyces cerevisiae gene-deletion mutants in pooled cultures. Nat Protocols 2: 2958-2974]
P-GSE46145-3
nucleic acid extraction protocol
Genomic DNA was extracted bu using the YeaStarTM Genomic DNA Kit (Zymo Research).
P-GSE46145-2
growth protocol
Bioreactors containing 200 mL of the previously described synthetic must were inoculated to an initial OD600 of 0.2. Cultures were grown in batch mode during about 12 h prior to triggering the continuous cultures. According to the data obtained from batch characterization, dilution rate was set to 0.23 h-1 for competitions mimicking Phase I and to 0.04 h-1 for those mimicking Phase II. Competition experiments using the heterozygous collection were run for 20 generations (corresponding to 60 h for Phase I or 347 h for Phase II) while those performed with the homozygous collection were run for 10 generations (30 h for Phase I or 174 h for Phase II). Yeast cell samples were taken at the onset of the continuous cultures, and after the indicated numbers of generations, in order to compare pool compositions at the beginning and the end of the competition experiments. Additional triplicate competition experiments, using YPD broth (D=0.23 h-1), were performed in order to differentiate deletions unspecifically affecting yeast growth from those specific for Phase I or Phase II fermentation conditions.