a definition of experimental and assay batch factors). Confidence intervals for the Cellomics variance components were obtained with the ‘profile’ method implemented in the ‘confint’ function of the lme4 package. The following random effects were included for each assay: Methylation - Donor. Experimental factors (summed up to produce Fig. 3a): gender, passage interval at time of assay. Assay batches (summed up to produce Fig. 3a): sentrix id, sentrix array (within sentrix id), bisulfite conversion plate, year and month of assay, year and month of Tier 1 assays.Expression microarrays - Donor. Experimental factors: gender, passage interval at the time of assay, culture system at time of assay, trisomy status, recurrent CNA status. Assay batches: array batch, year and month of assay, beachip id, beadchip array (within beadchip id), technician id, assay performed before or after April 2014.RNA-seq - Donor. Experimental factors: gender, passage interval at time of assay, trisomy status, recurrent CNA status, culture system at time of assay. Assay batches: year and month of assay, year and month of Tier 1 assays.Proteomics (uniquely identified proteins) - Donor. Experimental factors: gender. Assay batches: year and month of QC assays, instrument, year and month of analysis.Cellomics - Donor. Experimental factors: gender, culture
