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Table 3 Comparison of Cq values obtained using RNA isolated with the old vs. the new protocol

From: An optimised protocol for isolation of RNA from small sections of laser-capture microdissected FFPE tissue amenable for next-generation sequencing

Primer Sample Mean Cq old Mean Cq new Δ Mean Cq new – mean Cq old
GAPDH #2 Normal 26.99 26.56 −0.43
#2 Tumour 24.89 24.61 −0.29
#3 Tumour 22.24 17.75 −4.49
#4 Tumour 22.99 19.23 −3.75
#5 Normal 26.74 24.40 −2.34
#6 Tumour 20.97 20.98 0.00
#7 Tumour 23.57 19.79 −3.78
#8 Normal 23.72 23.28 −0.44
#9 Normal 27.36 27.77 0.41
#9 Tumour 24.82 19.33 −5.49
#10 Normal 27.29 26.89 −0.40
#10 Tumour N.d. 25.68 n.a.
  Mean ΔCq New−Cq Old for GAPDH −2.06
B2M #2 Normal 25.83 24.62 −1.21
#2 Tumour 21.88 21.27 −0.61
#3 Tumour 22.76 17.48 −5.28
#4 Tumour 22.70 18.83 −3.87
#5 Normal 24.33 21.38 −2.95
#6 Tumour 21.32 21.07 −0.25
#7 Tumour 23.89 18.87 −5.02
#8 Normal 24.13 24.46 0.33
#9 Normal 27.63 26.14 −1.49
#9 Tumour 25.94 21.36 −4.58
#10 Normal 28.98 26.73 −2.25
#10 Tumour 27.92 24.16 −3.76
  Mean ΔCq New−ΔCq Old for B2M −2.59
  1. Identical amounts of RNA were reverse transcribed and analysed by RT-qPCR using GAPDH or B2 M primers. First column: primers that were used for the analysis. Second column indicates the case and type of tissue from which the RNA that was analysed derived. “Mean Cq Old” denotes the mean Cq values obtained with RNA isolated using the old extraction protocol. “Mean Cq New” shows the Cq values obtained with RNA isolated using the new extraction protocol. “Δ Mean Cq New-mean Cq old” shows the difference in Cq values between the new extraction protocol and the old extraction protocol; a negative value here indicates better performance (lower Cq values) of the new extraction protocol. “Mean Δ Cq New-Cq old values” for GAPDH and B2 M list the mean difference of the Cq values between new and old extraction across all samples. N.d not detectable, n.a not applicable.