Table 1.
The design and experimental performance of nineteen staggered probe sets used to detect a 104 bp genomic DNA deletion in an A. thaliana mutant
| Probe set staggering (bp) |
Number of probes |
% of probes with a log 2 normalized ratio of ≤ −0.4 | |
|---|---|---|---|
| Designed | Detected with a log 2 normalized ratio of ≤ −0.4 | ||
| 2 |
77 |
66 |
86 |
| 6 |
25 |
22 |
88 |
| 10 |
15 |
14 |
93 |
| 12 |
12 |
12 |
100 |
| 15 |
10 |
9 |
90 |
| 17 |
9 |
8 |
89 |
| 20 |
8 |
7 |
88 |
| 22 |
7 |
7 |
100 |
| 25 |
6 |
6 |
100 |
| 27 |
5 |
5 |
100 |
| 30 |
5 |
4 |
80 |
| 32 |
5 |
5 |
100 |
| 35 |
5 |
5 |
100 |
| 37 |
4 |
4 |
100 |
| 40 |
4 |
4 |
100 |
| 42 |
4 |
3 |
75 |
| 45 |
3 |
3 |
100 |
| 47 |
3 |
3 |
100 |
| 49 | 3 | 3 | 100 |
Table 1 The table shows the staggered design of probes that cover a 104 bp phyB deletion in the E124 A. thaliana mutant line. The number of probes in each staggered probe set that covered the deletion are shown (column titled ‘Designed’). The number and percent of ‘Designed’ probes that were experimentally detected with normalized log2 intensities of ≤ −0.4 are also shown.