Total RNAs from CEM cells with or without Dex treatment for 24 h were subjected to the expression array analysis using Illumina BeadChip (San Diego, CA, USA).
For each DNA sample subjected to the Bioplex array assay, median fluorescence intensity (MFI) values were generated for each of the 44 microsphere populations corresponding to each allele within the assay.
Yet, if the complete method is applied (i.e. if the data are also subjected to the between-array normalization component of the technique), the data quality can be strongly degraded in some cases (see the next part 'Between-array Normalization' and Figure 4).
For analysis of Ig secretion, 50 μl of day 7 culture supernatants were subjected to the cytometric bead array (CBA) using Mouse Immunoglobulin Isotyping Kit (BD Biosciences, San Jose, CA, USA) according to the manufacturer's instructions.
Markers with significantly different mean serum concentrations in cancer patients and normal subjects were selected and subjected to the 35-plex bead array panel.
After DNA purification, bisulphite-converted DNA samples were randomly arrayed and subjected to the Infinium HumanMethylation27 BeadChip panel array-based assay.
Raw data were subjected to the frozen Robust Multi-Array Average (fRMA) algorithm56, followed by summarization based on multi-array model, fitted using the Median Polish algorithm.
The conditional media were further concentrated by the centrifugal filter devices (Amicon Ultra-4, 3 k, Millipore) to 100-fold concentrated volume and then subjected to the human cytokine antibody arrays (G series 2000, RayBiotech).
For each sample, a mixture of TaqMan Gene Expression Master Mix and cDNA equivalent to 250 ng total RNA was loaded onto the array and subjected to the amplification of 93 immune- or inflammation-related genes plus three endogenous controls.
The modified Gene Array groups could then be subjected to the same PLIER summarization step as the Exon Array data.
The objective function is subjected to the following constraints: begin{array}{*{20}l} sum_{q in Q} X_{vq}&=1, qquad v in VM, end{array} (2).
