RNA was extracted from four to five 5-um sections using an RNA extraction kit (Roche High Pure RNA Paraffin kit), yielding 0.5 - 3 ug of total RNA.
Label
Cy5
Label protocol
GoldenGate® assay was done as described previously (Fan JB et al, Illumina Universal bead arrays, 2006)
Hybridization protocol
Array image processing and signal extraction were done as described previously (Fan JB et al, Illumina Universal bead arrays, 2006)
Scan protocol
Arrays were imaged using Illumina BeadArray Reader scanner (Illumina).
Description
none
Data processing
Image analysis and data extraction software were as described previously (Oliphant, A., Barker, D.L., Stuelpnagel, J.R., and Chee, M.S. 2002. BeadArray technology: enabling an accurate, cost-effective approach to high-throughput genotyping. Biotechniques 32: S56-S61.; Galinsky, V.L. 2003. Automatic registration of microarray images II: Hexagonal grid. Bioinformatics 19: 1832-1836.). Each sequence type is represented by an average of thirty beads on the array. Bead signals are computed with weighted averages of pixel intensities, and local background is subtracted. Sequence-type signal is calculated by averaging corresponding bead signals with outliers removed (using median absolute deviation).
