Table 2.
RNA-seq experiment validation by RT-qPCR. RPKM: reads per kb per million reads; FDR: false discovery rate; SE: standard error. The p value was calculated by the SPSS software.
| Gene ID | RNA-seq | RT-qPCR | ||||
|---|---|---|---|---|---|---|
| RPKM | FDR | 2-ΔCT (mean ± SE) | p value | |||
| Orange | White | Orange | White | |||
| Bra035683 | 9.18 | 3.68 | 2.30E − 05 | 0.0070 ± 0.00023 | 0.0073 ± 0.00115 | 0.812 |
| Bra039047 | 0.09 | 4.26 | 2.03E − 11 | 0.0009 ± 0.00007 | 0.0426 ± 0.00036 | 0 |
| Bra011759 | 1.54 | 10.23 | 1.13E − 16 | 0.0004 ± 0.00002 | 0.0189 ± 0.00185 | 0.01 |
| Bra010598 | 0.99 | 6.14 | 2.31E − 09 | 0.0002 ± 0.00001 | 0.0112 ± 0.00068 | 0.004 |
| Bra004735 | 0.81 | 4.43 | 0.000355 | 0.0005 ± 0.00004 | 0.0329 ± 0.00257 | 0.006 |
| Bra025756 | 15.30 | 44.25 | 1.74E − 22 | 0.0020 ± 0.00021 | 0.0233 ± 0.00091 | 0 |
| Bra031132 | 3.12 | 7.98 | 0.00027 | 0.0044 ± 0.00012 | 0.0067 ± 0.00015 | 0 |
| Bra024643 | 6.58 | 16.11 | 2.31E − 07 | 0.0130 ± 0.00076 | 0.0232 ± 0.00178 | 0.006 |
| Bra039555 | 10.39 | 23.40 | 1.82E − 10 | 0.0043 ± 0.00025 | 0.0199 ± 0.00313 | 0.037 |
| Bra040203 | 8.33 | 16.68 | 8.20E − 05 | 0.0425 ± 0.00138 | 0.1340 ± 0.01970 | 0.01 |
| Bra031539 | 2.71 | 3.34 | 0.732593 | 0.0155 ± 0.00059 | 0.0170 ± 0.00130 | 0.373 |