Table 3. RNA integrity and microarray quality controls.
| RNA integrity | Microarray quality controls | ||||||
|---|---|---|---|---|---|---|---|
| Tissue (specimen) |
RIN# |
260/280 |
Average background |
Noise (Raw Q) |
GAPDH 3′/5′ ratio |
% present calls |
|
| Macula (1) |
8.9 |
2.03 |
89.8 |
3.6 |
1.09 |
51.4 |
|
| Nasal (1) |
9 |
2.03 |
89.3 |
3.55 |
1.15 |
50.8 |
|
| Surround (1) |
9.3 |
2 |
88.4 |
3.54 |
1.1 |
51.5 |
|
| Macula (2) |
9.5 |
2.04 |
90.8 |
3.6 |
1.09 |
50.1 |
|
| Nasal (2) |
9.9 |
1.96 |
82.8 |
3.32 |
1.12 |
50.9 |
|
| Surround (2) |
9.2 |
2.08 |
91.8 |
3.62 |
1.14 |
50.6 |
|
| Macula (3) |
9.1 |
1.97 |
80 |
3.05 |
1.21 |
51.9 |
|
| Nasal (3) |
9 |
1.97 |
73.4 |
2.83 |
1.16 |
55.5 |
|
| Surround (3) |
8.7 |
2.02 |
59.7 |
2.43 |
1.05 |
54.2 |
|
| Macula (4) |
9 |
1.85 |
53.9 |
2.19 |
1.13 |
54.6 |
|
| Nasal (4) |
9.3 |
1.97 |
57.5 |
2.37 |
1.14 |
54.9 |
|
| Surround (4) | 8.8 | 2.06 | 64.9 | 2.59 | 1.15 | 55.7 | |
Integrity measures of RNA samples showed the samples were of appropriate purity for hybridization to microarrays. The RIN was high, ranging from 8.4 to 9.9, and the 260/280 ratios were also high, ranging from 1.85 to 2.08. Microarray quality controls were within manufacturer recommendations and control values were comparable between arrays. The sharp (hash mark) indicates that the RNA integrity number (RIN) ranges from 1 to 10, with 10 indicating no RNA degradation, relative to a database of approximately 1,300 total RNA samples of varying levels of integrity and derived from various tissues from human, rat and mouse [23].