In a previous study, microsomal proteins from biological duplicates of A. niger were separated by SDS-PAGE and gel slices were processed for LC-MS/MS (Ferreira de Oliveira et al. 2010).
Biological duplicates of the inoculations were performed with the lysates used in triplicate reporter assays.
RNAs extracted from biological duplicates of these cultures were labeled then profiled on Affymetrix Human Gene ST 1.0 Array Gene Chips.
Three biological duplicates of each sample and triplicates of each reaction were acquired.
D-REAM analysis was performed twice for each of the biological duplicates of heart, and once for the liver and brain in this study.
Hybridizations of the biological duplicates of each experiment were carried out in technical duplicates using dye swaps (Cy3 and Cy5), for a total of 4 replicates for each of the overexpression and downregulation experiment.
The top group (quadrant I) consists of data from both behaviorally addicted (black) and nonaddicted rats (red), while the other group (quadrant IV) comprises data generated from biological duplicates of behaviorally nonaddicted rats (multiple points due to technical replicates).
Briefly, biological duplicates of each tissue (i.e. Retina, Lens, Cornea, RPE; labeled with Hy3) and RNA from entire eyes (labeled with Hy5) were hybridized on the same slide.
In addition to the published dataset (NCBI Gene Expression Omnibus (GEO) accession GSE60019), we also added unpublished gene expression results of hair cells and non-hair cells from P16 mouse utricles as well as a validation study with a biological duplicate of E16 mouse cochleae and utricles.
To take account of the expression variability due to cellular heterogeneity, totRNA was extracted from a biological duplicate of both normal and tumour specimens.
A gene was defined as "expressed" when ≥50% of probesets of the same gene had a DABG p-value of ≤0.05 in both biological duplicate of the same time point [19], [26].
