Dataset features


Application: Gene expression microarray analysis
Number of samples: 20
Release date: Jul 6 2006
Last update date: Mar 16 2012
Access: Public
Chemicals: Nitrogen, Glutamic Acid, Sirolimus
Dataset link Transcriptional response to nitrogen availability in yeast

Experimental Protocol

The hybridization signal was measured using a GSM418 laser scanner. Image analysis for each array was processed using the GenePix Pro 4.0 (Axon Instruments, Inc.) software package, which measures fluorescence intensity pairs for each gene. Following image acquisition, a visual inspection of the individual spots on each microarray (size, signal-to-noise ratio, background level, and spot uniformity) completed the flagging (present/not present, good/bad) of the data. To maximize sensitivity two scans were made, one at high laser power and high PMT (Photo Multiplier Tube) gain to detect the faintest spots, and a second one using low laser power and a PMT gain avoiding saturation. The values for spots presenting ≥ 5% saturation in the first scan were calculated based on an extrapolation after linear regression analysis of the intensities from both scans. These data were then imported in the GeneSpring 7.1 (Silicon Genetics) software package, applying a per spot per chip intensity-dependent (Lowess) normalization for further analysis.