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Table 2 Copy number estimation of SINE by quantitative RT-PCR

From: Multiple source genes of HAmo SINE actively expanded and ongoing retroposition in cyprinid genomes relying on its partner LINE

Standard Serial Con CT Cultivation:
Plasmid (Hmo_41) 0.2 μg/μl 11.10 Y = -0.2989x+14.22
  0.02 μg/μl 16.30 Y = -0.2989x+14.22
  0.002 μg/μl 18.36 R ^2 = 0.997; E = 0.99
  0.0002 μg/μl 21.72 Results:
plasimid DNA size = 2× 103 bp
copy number of plasmid per μl
= 6.5× 1011 (2 ug/ul)
  0.00002 μg/μl 25.30   
Sample Con/(ug/ul) CT PCNH Avg.
Xenocypris argentea 0.115 13.32 183221.1127 3.0 × 105
  0.0115 15.44 425899.8786  
Cutler alburnus 0.9 12.12 53470.08164 3.5× 104
  0.09 17.11 17242.48462  
Elopichthys bambusa 0.133 15.32 39996.47484 4.0 × 104
  0.0133 18.69 39330.43191  
Squaliobarbus curriculus
(Genome size≈ 1 pg)
0.1 13.83 148331.8306 1.7 × 105
  0.01 16.8 192088.4962  
Mylopharyngodon piceus
(Genome size≈ 1 pg)
0.36 15.04 17916.89943 1.7× 104
  0.036 18.46 17022.5593  
Ctenopharyngodon idellus
(Genome size≈ 1 pg)
0.314 15.32 16941.18202 1.7 × 104
  0.0314 18.69 16659.06829  
Leuciscus tumensis 0.104 13.32 202600.2689 3.3× 105
  0.0104 15.44 470946.9811  
Saurogobio dabryi 0.03 11.91 1853536.326 1.7× 106
  0.003 15.51 1555826.276  
Rhodeus ocellatus
(Genome size≈ 1 pg)
0.092 13.91 152592.9712 2.2× 105
  0.0092 16.23 309091.1208  
Cyprinus carpio
(Genome size≈ 2 pg)
0.0033 22.06 31174.78108 3.1× 104
  0.00033 25.39 31511.30668  
Shizothorax grahami 0.08 10.66 3286149.864 5.1× 106
  0.008 12.87 7179899.5  
  1. Con: concentration; CT: (cycle threshold) is defined as the number of cycles required for the fluorescent signal to cross the threshold; PCNH: Predicted copy no. in haploid genome; SC: standard curve; The R2 value is the coefficient that is used to assess the fit of the standard curve to the data points plotted. The R2 value was > 0.99 which is the required value for reliable quantitation. The efficiency of the PCR reaction (E) is calculated using the formula E = (10(-1/slope)- 1), where the slope is calculated from a standard curve plot of Ct values against the logarithm of template amount. A value close to 1 indicates high PCR efficiency. PCNH was calculated using the equation: PCNH = Genome size (pg)/Genomic DNA Con (μg/μl) × 10Y/10 21.72× 6.5× 107. The genome size information came from http://www.genomesize.com/.