200 ng of total RNA provided by the MAQC were amplified and labeled using the Illumina(R) TotalPrep(TM) RNA Amplification kit (Ambion; catalog #IL1791).
Hybridization protocol
Illumina Human-6 whole genome microarrays (Illumina; catalog # BD-25-101) were hybridized to 1.5 micrograms of labeled, amplified material, and then washed, stained, and scanned according to the protocol described in the Illumina Whole Genome Gene Expression for BeadStation Manual, Revision D.
Scan protocol
Scanning software was BeadScan 2.3.0.10.
Description
NA
Data processing
Data was processed using Illumina BeadStudio version 1.5.0.34 software using background subtraction and cubic spline normalization.
Data were quantile-normalized per test site (20 arrays). Normalized hybridization intensity values were adjusted by adding a constant such that the lowest intensity value for any sample equaled 16.
