Table 1.
cRNA Yield and Hybridization Results
| Source | Input | Method | Yield (ug) | 3′/5′ | SF | % Genes = P | ||||
|---|---|---|---|---|---|---|---|---|---|---|
| No. 1 | No. 2 | No. 1 | No. 2 | No. 1 | No. 2 | No. 1 | No. 2 | |||
| Breast cancer | 10 ug | Standard (A) | 40 | 46 | 3.1 | 3.4 | 1.0 | 1.1 | 55 | 55 |
| An3Ca cell line | 2 ug | Standard (A) | 24 | 22 | 1.0 | 1.1 | 0.8 | 0.6 | 51 | 54 |
| G401 cell line | 2 ug | Standard (A) | 24 | 22 | 1.0 | 1.1 | 1.8 | 1.3 | 54 | 53 |
| NI. heart | 2 ug | Standard (A) | 18 | 20 | 1.3 | 1.2 | 1.4 | 1.4 | 56 | 54 |
| An3Ca cell line | 2 ug | RiboAmp 1 Round (B) | 60 | 56 | 3.1 | 3.5 | 0.7 | 1.2 | 51 | 47 |
| G401 cell line | 2 ug | RiboAmp 1 Round (B) | 86 | 74 | 4.5 | 5.3 | 1.5 | 1.6 | 49 | 46 |
| NI. heart | 2 ug | RiboAmp 1 Round (B) | 72 | 68 | 4.7 | 4.1 | 1.2 | 2.5 | 43 | 49 |
| Breast cancer | 10 ng | Standard 2 Round (C) | 16 | 16 | 4.4 | 4.0 | 5.8 | 4.2 | 36 | 40 |
| Breast cancer | 10 ng | RiboAmp 2 Round (D) | 36 | 24 | 49 | 55 | 3.5 | 2.2 | 40 | 43 |
| An3Ca cell line | 10 ng | RiboAmp 2 Round (D) | 53 | 47 | 43 | 66 | 2.7 | 5.4 | 36 | 35 |
| Normal, heart | 10 ng | RiboAmp 2 Round (D) | 55 | 26 | 57 | 50 | 7.8 | 4.4 | 32 | 35 |
| G401 cell line | 10 ng | RiboAmp 2 Round (D) | 54 | 43 | 66 | 51 | 3.0 | 5.0 | 37 | 36 |
| LCM breast 1 | 30 ng | RiboAmp 2 Round (D) | 40 | 40 | 25 | 33 | 1.1 | 1.7 | 44 | 39 |
| LCM breast 2 | 30 ng | RiboAmp 2 Round (D) | 18 | 18 | 30 | 67 | 2.1 | 5.4 | 43 | 36 |
Source, source of RNA; input, amount of total cellular RNA used for target synthesis; method, method used to generate biotinylated cRNA (see materials and methods); yield, yield of purified cRNA from two, duplicate target synthesis reactions; 3′/5′, ratio of hybridization signals obtained from GeneChip probe pair sets directed at the 3′ or 5′ end of GAPDH transcript; SF, scale factor utilized to generate an average signal intensity of 150 using Microarray Analysis Suite (MAS) 4.0 software; % genes = P, percentage of genes scored detected (“P”) by MAS 4.0.