Table II.
Probe set signal intensities and 3′ to 5′ ratios of housekeeping genes for the Barley1 GeneChip probe array.
| Probe Set Name
|
Description (NCBI BLASTn Hit)
|
Signal Intensitya
|
Remarks
|
|||
|---|---|---|---|---|---|---|
| 5′ | Middle | 3′ | 3′ to 5′ Ratio ± sdb | |||
| Contig333 | Barley α-tubulin (tuba; 0.0) | 3,381 (333_5_at)c | 4,306 (333_M_at) | 2,334 (333_3_x_at) | 0.73 ± 0.15 | Similar signal intensity across all regions of the transcript |
| Contig865 | Barley glyceraldehyde-3-phosphate dehydrogenase (0.0) | 2,792 (865_5_s_at) | - | 5,336 (865_3_s_at) | 1.89 ± 0.30 | 5′ Region produced slightly lower signal intensity as compared with 3′ |
| Contig2580 | Rice translation initiation factor 5A (e-122) | 2,096 (2580_5_s_at) | - | 1,891 (2580_3_at) | 0.84 ± 0.16 | Of the two probe sets tiled for the 5′ region, contig2580_5_s_at showed signal similar to 3′ contig2580_3_at |
| Contig1390 | Barley actin (0.0) | 583 (1390_5_at) | 5,654 (1390_M_at) | 6,975 (1390_5_s_at) | 1.07 ± 0.22 (3′/middle) | Very little signal detected from 5′ probe set; recommend use of 3′ to middle ratio |
a
Average of 100 GeneChip probe arrays
b
Average 3′ to 5′ ratio ± sd based on 100 GeneChip probe arrays
c
Denotes specific probe set within designated contig