8 protocols
AccessionType
bioassay_data_transformation
ID_REF = VALUE = Robust mean Log2 intensity for replicate features calculated with S-plus/R function
feature_extraction
Robust mean Log2 intensity for replicate features calculated with S-plus/R function. Up and down tags are processed separately and output reported as separate data sets. Note: Platform GPL8633 contains the array design which will be helpful for users who do not want to use our preprocessing strategy.
image_aquisition
After hybridization, arrays were stained and scanned at an emission wavelength of 560 nm using a GeneChip scanner (Affymetrix)
hybridization
Reactions hybridized overnight to custom-built TAG4 microarrays (Affymetrix)
labeling
The strain-specific barcodes contained in the DNA were amplified by PCR using a set of biotinylated primers
grow
Growth in YPD (rich) media, 30 °C, 200 rpm. Measurements of optical density at 595 nm (OD595) to monitor growth
specified_biomaterial_action
Chemical treatments incorporated into growth media, 3 concentrations with 3 biological replicates each, for 5 and 15 generations (g) of growth
nucleic_acid_extraction
Cells were collected and genomic DNA was extracted using the YDER kit (Pierce Biotechnology)