Table 1 Design of spike-in experiment. The spike-in controls are two sets of ten synthesized RNA mixtures derived from the Adenovirus E1A transcriptome [31] with different concentrations in each set. The A mix was hybridized with Cy3 and the B Mix with Cy5 on each array, according to manufacturers recommendations, and in the recommended quantity.
RNA spike-in name | A Mix relative copy number | B Mix relative copy number | expected ratio A/B |
|---|---|---|---|
(+)E1A_r60_1 | 10 | 10 | 1:1 |
(+)E1A_r60_n11 | 1.5 | 0.5 | 3:1 |
(+)E1A_r60_a20 | 100 | 100 | 1:1 |
(+)E1A_r60_3 | 3 | 9 | 1:3 |
(+)E1A_r60_a104 | 10 | 30 | 1:3 |
(+)E1A_r60_a107 | 30 | 10 | 3:1 |
(+)E1A_r60_a135 | 9 | 3 | 3:1 |
(+)E1A_r60_a22 | 10 | 100 | 1:10 |
(+)E1A_r60_a97 | 0.5 | 1.5 | 1:3 |
(+)E1A_r60_n9 | 100 | 10 | 10:1 |