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Table 3 Comparative data of RT-qPCR and RNA-Seq for 7 differentially expressed conserved miRNAs

From: Systematic miRNome profiling reveals differential microRNAs in transgenic maize metabolism

miRNA Comp. Samples Ct Rep. 1 Ct Rep. 2 Ct Rep. 3 Read count Log2FC RT-qPCR Log2FC RNA-Seq
zma-MIR167c Bt
vs
Control
Bt S1 26.59 26.56 26.68 103 0.58 0.56
Bt S2 26.67 26.49 26.62 304
Bt S3 26.66 26.37 26.38 230
Conv S1 27.33 27.31 27.58 199
Conv S2 27.53 27.85 27.69 132
Conv S3 27.39 26.97 26.79 170
zma-MIR167ej Bt
vs
Control
Bt S1 26.22 26.17 26.11 325 0.11 0.55
Bt S2 25.99 25.95 25.93 515
Bt S3 26.11 26.17 26.10 428
Conv S1 26.46 26.53 26.54 336
Conv S2 26.55 26.65 26.49 293
Conv S3 26.24 26.31 26.11 380
zma-MIR169f Bt
vs
Control
Bt S1 26.81 26.34 26.27 108 − 1.05 − 0.78
Bt S2 26.35 26.87 27.07 118
Bt S3 26.43 26.13 26.73 170
Conv S1 25.11 24.88 25.09 77
Conv S2 26.61 25.63 25.76 176
Conv S3 26.80 26.84 26.62 115
zma-MIR169 m Bt
vs
Control
Bt S1 28.12 27.99 28.14 561 0.42 0.62
Bt S2 27.36 27.42 27.53 852
Bt S3 27.56 27.81 27.14 642
Conv S1 28.95 28.27 28.51 447
Conv S2 28.33 28.41 27.90 617
Conv S3 28.40 28.27 27.89 433
zma-MIR399ah Bt
vs
Control
Bt S1 29.68 29.44 29.75 26 − 0.29 − 0.70
Bt S2 29.43 29.36 29.14 48
Bt S3 29.22 29.34 29.12 34
Conv S1 29.41 29.09 28.90 55
Conv S2 29.69 29.19 29.62 40
Conv S3 28.98 29.99 28.99 44
zma-MIR399eij RR×Bt
vs
Control
RR×Bt S1 22.15 22.09 22.12 63 − 1.51 − 0.64
RR×Bt S2 22.27 22.35 22.31 91
RR×Bt S3 22.47 22.36 22.29 107
Conv S1 20.61 20.66 20.72 116
Conv S2 21.09 21.08 21.07 107
Conv S3 20.71 20.71 20.82 165
zma-MIR399eij RR×Bt
vs
RR
RR×Bt S1 22.15 22.09 22.12 63 0.00 − 0.86
RR×Bt S2 22.27 22.35 22.31 91
RR×Bt S3 22.47 22.36 22.29 107
RR S1 23.11 23.09 23.14 146
RR S2 22.10 22.07 22.16 203
RR S3 23.39 23.46 23.41 150
zma-MIR827 RR×Bt
vs
Control
RR×Bt S1 27.27 26.97 26.99 479 − 0.58 − 0.54
RR×Bt S2 27.33 27.35 27.52 552
RR×Bt S3 27.37 27.35 27.25 554
Conv S1 26.92 26.84 26.63 683
Conv S2 26.53 26.87 27.18 602
Conv S3 26.98 26.53 26.67 675
zma-MIR827 RR×Bt
vs
RR
RR×Bt S1 27.27 26.97 26.99 479 − 1.00 − 0.50
RR×Bt S2 27.33 27.35 27.52 552
RR×Bt S3 27.37 27.35 27.25 554
RR S1 26.69 26.64 26.70 656
RR S2 26.80 26.81 27.00 718
RR S3 26.74 26.59 26.54 751
  1. zma-miR162 and zma-miR529 are not included in the table due to multiple melting curve peaks on the RT-qPCR. Comp. comparison, Ct cycle threshold, Rep. replicate, FC fold change, Control conventional non-transgenic sample, Bt MON89034 transgenic event sample, RR NK603 transgenic event sample, RR×Bt stacked transgenic event