Regardless, the microarray experiments did not confirm the differential expression of the frd operon, as detected by BACFA analysis and confirmed by qRT-PCR.
AR performed the microarray experiments, did the mice infections, prepared all Figures and Tables, and participated in the analysis of the data and the writing of the manuscript.
Given the many caveats of the data at the time the Lee et al. ChIP-chip data were collected only in YPD and the microarray experiments did not contain all possible environmental perturbations this finding paints a relatively optimistic picture regarding the functionality of individual TF binding sites.
The development of Liverome was initiated to compare our own gene signatures derived from microarray experiments done on a large HCC cohort in Korea (through "The 21C Frontier Functional Human Genome Project of Korea") with publicly reported gene signatures.
PC and VW conceived the experiments, VW and DJM grew the plants and carried out the UV-B experiments, DJM did RNA, protein and metabolite extractions, DJM did the RNA labeling and microarray hybridizations, JF and PC analyzed the microarray experiments, MC did the proteomic experiments, PC did the metabolomic analysis.
All the experiments (except microarray experiment) were done for three times.
Each microarray experiment was done with two technical replicates by reversing dye hybridization for experimental and reference samples.
Technically, for each comparison, the microarray experiment was done twice, one using different biological samples, each consisting of a sample pool from 3 animals.
In microarray experiments, we did not detect significant differences in white transcription between su(wsp 1 wsp1 and wsp1 adults, confirming the conclusion of the two earlier studies that altered white transcription does not appear to be responsible for the reduction in eye pigmentation (Wasser and Chia, unpublished).
Considering the complexity of the processes involved in microarray experiments, we did not expect that the coefficient would be constant even for just a variety of RNA samples of a given type of array.
