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validation technology comparison
The UHNMAC offers several technologies for validating the data obtained from high-density microarray experiment: Bio-Plex, Nanostring and Ziplex. These three new technologies enable highly-multiplexed microarray data validation.
Quantitative PCR is considered the gold standard technique for validating microarray results, although this technique can be labourious and costly if you have a large number of genes or samples that require validation.
Please note that we do not offer a qPCR service.
| qPCR | Bio-Plex | Nanostring | Ziplex (Xceed) | |
| Advantages |
Gold standard
TaqMan probes available for most genes |
Highly multiplexed
Also capable of protein assays |
No enzymology
Highly multiplexed |
Array-based method (similar protocol and data format to high-density arrays) |
| # genes requiring validation | < 20 | 20-80 | 30-500 (and for >96 different samples, or multiples of 12 if using catalog CodeSets) | 20-120 |
| Theoretical maximum # of genes per sample (per run), including controls | 4 | 100 | 550 | 400 |
| Practical # of genes per sample (per run) | 1 | 80 | 500 | 120 |
| Amount of total RNA required |
1-100 ng | coming soon | 100 ng | 500 ng |
| Detection limit | <1 copy per cell (<0.5 fM) |
coming soon | <1 copy per cell (<0.5 fM) |
approx. 400 copies per cell (0.2 pM) |
| Dynamic range | 2 logs (100-fold) | coming soon | 3 logs (but as high as 6 logs) |
3 logs |
| Works with degraded RNA? |
No | Good results from FFPE samples provided >50% had length > 300 bp | ||
| # different samples processed simultaneously (per run) | 96 or 384 | 96 | 12 | 8 |
| Time per run | 5 hours | coming soon | 18 hours (including 12 hour overnight hyb) | 3 hours + approx. 20 hours for IVT reactio |