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Analysis of Microarray Data

rformed with each sample RNA and the quantified data was represented as slide averages resulting in 12 arrays for each aRNA and mRNA sample. Images were acquired using a Molecular Dynamics Array Scanner. Microarray data analysis was performed using Spotfire Software (Spotfire, Somerville, MA).


Cluster Analysis
An example of the image data obtained from 4 of the 12 grids from a standard 6912 element HCI array is represented in Figure 1. Comparison of the signals obtained using mRNA vs. aRNA indicates that RNA amplification provides excellent signal to noise, even for genes with a low level of expression.

Figure 1. Array Analysis of 6912 Element Arrays. Image Data from 4 of the 12 grids of a standard 6912 element Hunstman Cancer Institute cDNA microarray. mRNA or aRNA (2 g) was reverse transcribed in the presence of random ninemers and Cy dyes. HCT 116 samples were labeled with Cy5-dCTP while RKO cells were labeled with Cy3-dCTP. Analysis of the microarray data was carried out using Spotfire Software (Spotfire, Somerville, MA).

mRNA Sample A260/280 aRNA Yield RKO-1 2.12 37.0 g RKO-2 2.15 28.7 g RKO-2 2.12 26.8 g HCT116-1 2.12 33.5 g HCT116-2 2.12 36.2 g HCT116-3 2.12 29.5 g

Figure 2. Yields of Amplified RNA. Yields obtained a
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