Table 2

Calibration curves and strains used for the Taq nuclease assay and the TaqMan genotyping assay (SNP).

TNA

Gene locus

Strain

Calibration curvea

E (%)b

R2 c

n

Quantification limit

(cells per template)d

Amplicon

length (bp)


16S

16S rDNA

PCC7821

y = 11.021 - 3.5123x

92.6

0.997

12

4

82

PC-IGS

Intergenic spacer of the phycocyanin operon

PCC7821

y = 9.9401 - 3.5673x

90.7

0.994

12

4

72

mcyB

First adenylation domain of mcyB

PCC7821

y = 12.151 - 3.3745x

97.9

0.993

11

4

76

mcyDIS1

3'-end of IS-element within mcyD

No.110

y = 7.941 - 3.8823x

81.0

0.994

12

4

93

mcyDIS2

3'-end of IS-element within mcyD

No.139

y = 11.956 - 3.1314x

108.6

0.980

11

18

110

mcyAIS

3'-end of IS-element within mcyA

No.40

y = 11.126 - 3.6644x

87.5

0.991

11

4

168

mcyHA

Deletion between mcyH and mcyA

No.62

y = 14.648 - 3.751x

84.8

0.996

12

4

71

PSA I (lineage 1)e

Intergenic spacer between psaA and psaB

PCC7811

y = 14.144 - 3.4482x

93.2

0.996

11

3

167

PSA II (lineage 2)e

Intergenic spacer between psaA and psaB

PCC7821

y = 13.681 - 3.3161x

100.2

0.978

9

4

158

SNP Assay allele 1

SNP within mcyT (genotypes that lost the mcy gene cluster)

PCC7811

y = 10.449 - 3.6685x

98.2

0.996

15

2

66

SNP Assay allele 2

SNP within mcyT (genotypes containing the mcy gene cluster)

PCC7821

y = 15.875 - 3.3579x

98.5

0.996

15

2

66


a Calibration curve = regression line; y = number of PCR cycles at the threshold fluorescent value (Ct), x = amount of template DNA (expressed as log10 of mm3 biovolume per template). b Amplification efficiencies (E) were calculated from E = (10 -1/x -1) × 100 (%), x = slope of calibration curve. c R2 = coefficient of determination of calibration curve. d Quantification limit given as cell number equivalents represents the lower end of the calibration curve. e According to [4].

Ostermaier et al. BMC Biology 2012 10:100   doi:10.1186/1741-7007-10-100

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