Table 1.
Overview of the different experiments.
| Experiment | Constitutive Active MK5 | FKRP Knockdown | TAF4 Knockdown | |||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Labeling | CY5/CY3 | DIG | DIG | |||||||
| Microarray | KTH Rat27K Oligo m.a, OperonV3.0 Tecan HS 4800 Genepix 4000B Genepix Pro 6.1.0.2 | Applied Biosystems Mouse Genome Survey m.a.V2.0 DIG Labeling Applied Biosystems 1700 scanner | Applied Biosystems Human Genome Surveym. aV2.0 DIG Labeling Applied Biosystems 1700 scanner | |||||||
| Groups | Normal (Cy5) | MK5 Induced (Cy3) | Control (Both) | siRNA #1 | siRNA #2 | Scrambled | SiRNA | Scrambled | siRNA | Scrambled |
| Amount | 3 | 3 | 1 | 3 | 2 | 3 | 4 | 4 | 4 | 3 |
| Cell line | PC12 TetOff for MK5L337A | C2C12 | SK-N-DZ | HeLa | ||||||
| Requested Comparisons | 1. Normal vs MK5 Induced | 2. siRNA#1 vs Scrambled 3. siRNA#2 vs Scrambled |
4. siRNA vs Scrambled | 5. siRNA vs Scrambled | ||||||
| Blind analysis | Microarray facilityTromsø Loess normalization | UNIGEN (Trondheim) Quantile Normalization | UNIGEN (Trondheim) Quantile Normalization | |||||||
| 27468 reported of which 4007 in agreement | 0 | 0 | not submitted | 70 | ||||||
| Intensity dependent analysis | Both Quantile and no normalization | Applied Biosystems Inter-array normalization | Applied Biosystems Inter-array normalization | |||||||
| 1422 | 2977 | 576 | 661 | 2497 (22 validated through qPCR) | ||||||
| Overlap | 311, with 10 wrong in the standard analysis | 0 | 0 | not applicable | 65 | |||||