Supplementary Table 1:Summary of cERC Concentration and tERC Molar Ratio Used for Plotting Concentration-Response Curves in Figure 1

GEH
cERC / Concentration (pM) / cRNA Mass Ratio
LEUB / 0.05 / 1:2,048,000
HISB / 0.20 / 1:512,000
GND / 0.78 / 1:128,000
FIXB / 3.13 / 1:32,000
ENTF / 12.50 / 1:8,000
ARAB / 50.00 / 1:2,000
AFX
cERC / Concentration (pM) / cRNA Mass Ratio
AFFX-BioB / 1.5 / 1:100,000
AFFX-BioC / 5 / 1:30,000
AFFX-BioDn / 25 / 1:6,000
AFFX-CreX / 100 / 1:1500
AFX
tERC / tERC/polyA / Molar Ratio 1:
AFFX-LysX / 0.0000100 / 100000
AFFX-PheX / 0.0000200 / 50000
AFFX-ThrX / 0.0000400 / 25000
AFFX-DapX / 0.0001500 / 6667
AG1
tERC / tERC/polyA / Molar Ratio 1:
r60_3 / 0.000000008 / 125000000
r60_a104 / 0.000000080 / 12500000
r60_a107 / 0.000000800 / 1250000
r60_a135 / 0.000008000 / 125000
r60_a20 / 0.000026667 / 37500
r60_a22 / 0.000080000 / 12500
r60_a97 / 0.000266667 / 3750
r60_n11 / 0.000800000 / 1250
r60_n9 / 0.002666667 / 375
r60_1 / 0.008000000 / 125

Supplementary Table 1: Comparison of the various ERCs implemented in GE Healthcare, Affymetrix and Agilent platforms. Two types of external RNA controls (ERC) are implemented in these four commercial microarray platforms. The first type of ERC is added to the total RNA (tERC) before initiating the cDNA synthesis and IVT (in vitro transcription) steps of the RNA labeling procedure. The second type of ERC is added to the cRNA (cERC) just before the cRNA is placed into the hybridization mixture.Applied Biosystems (data not shown due to single concentration nature of the ABI ERCs) and Affymetrix platforms utilize both types of ERCs in their respective protocols. Agilent uses the tERC at concentrations that interrogate the lower and upper limits of assay signal detection. GE Healthcare recommends using either tERC or cERC depending upon the application, and the presented GEH_Rat TGx experiment utilized only the cERC.