Table 2.

qRT-PCR validation of RNA-seq data

Locus tag	qRT-PCR fold change (salt stress vs control)	RNAseq fold change (salt stress vs control)	RNAseq vs qRT-PCR p-value (salt stress)	qRT-PCR fold change (osmotic stress)	RNAseq fold change (osmotic stress)	RNAseq vs qRT-PCR p-value (osmotic stress)
CCI6_RS21730a	2.100e	2.360	0.840	1.100	−6.000	0.012d
CCI6_RS17915a	3.120e	3.240	0.960	1.820e	1.980	0.870
CCI6_RS19875a	2.500e	4.910	0.03d	3.011e	11.210	0.023d
CCI6_RS17580a	3.140e	3.480	0.870	2.120e	1.520	0.560
CCI6_RS16000a	1.890e	2.183	0.930	−0.500	−1.200	0.040d
CCI6_RS18570c	1.320	1.230	0.240	1.511	1.380	0.720
CCI6_RS06495c	1.400	1.500	0.450	−1.310	−2.020	0.220
CCI6_RS02325b	3.500e	3.840	0.830	2.800e	3.860	0.620
CCI6_RS12340c	−1.300	−4.000	0.023d	1.300	−9.000	0.026d
CCI6_RS08505a	3.230e	3.590	0. 753	1.150	1.051	0.972
CCI6_RS19950b	10.021	12.061	0.778	18.231	21.585	0.812

^aUp-regulated genes under salt stress according to RNA-Seq analysis

^bUp-regulated genes under both conditions according to RNA-Seq analysis

^cNon-differentially expressed genes in the study according to RNA-Seq analysis

^dIndicates that there is a statistically significant difference between fold change values determined by qPCR and RNA-seq

^eIndicates a statistically significant qRT-PCR fold change value

The fold change values (salt vs control or sucrose vs control) determined from the RNAseq experiment were compared with the fold change values obtained from qRT-PCR experiments. For the qRT-PCR experiments, the ∆∆C_t method was used to determine the fold change. The rpsA gene was used as the normalizer for all of the qRT-PCR experiments. The fold change values for the RNA-seq experiments are based on two biological replicates whereas the fold change values for the qRT-PCR experiments are based on three biological replicates