Transcriptome Analysis of Orange Head Chinese Cabbage (Brassica rapa L. ssp. pekinensis) and Molecular Marker Development

Table 2

RNA-seq experiment validation by RT-qPCR. RPKM: reads per kb per million reads; FDR: false discovery rate; SE: standard error. The value was calculated by the SPSS software.

Gene ID	RNA-seq			RT-qPCR
	RPKM		FDR	2^-ΔCT (mean ± SE)		value
	Orange	White		Orange	White
Bra035683	9.18	3.68		0.0070 ± 0.00023	0.0073 ± 0.00115	0.812
Bra039047	0.09	4.26		0.0009 ± 0.00007	0.0426 ± 0.00036	0
Bra011759	1.54	10.23		0.0004 ± 0.00002	0.0189 ± 0.00185	0.01
Bra010598	0.99	6.14		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		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		0.0130 ± 0.00076	0.0232 ± 0.00178	0.006
Bra039555	10.39	23.40		0.0043 ± 0.00025	0.0199 ± 0.00313	0.037
Bra040203	8.33	16.68		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