DNA was quantified using standard PicoGreen protocols from Molecular Probes. Two of the 96-well plates were randomly chosen for the replication experiment at CIDR. Identical daughter plates were robotically generated (at concentrations appropriate for each technology, 50 ng/μl for Affymetrix and 100 ng/μl for Illumina). Because the performance of the Illumina assay is sensitive to low DNA concentration, replacements for 25 samples that contained less than 50 ng/μl of DNA were requested from Rutgers and included along with the original samples sent to Illumina. Plates were shipped to Affymetrix and Illumina for genotyping in their laboratories.
