Table 2

Five DNA extraction methods used: pure intact C. pneumoniae EB and aorta tissue samples spiked with C. pneumoniae EB For each sample type different EB input dilutions were used, these are displayed in the first column. Shown are also a rough estimate of the EB concentrations as determined by real-time PCR. For each method and sample the mean output C. pneumoniae genomic DNA concentration and standard deviation (SD) is displayed for two replicates as determined with the quantitative pmp4 LightCycler PCR. In addition relative recovery percent is calculated relative to the best method, which in this case was the MagNA Pure method (% Rel. rec.). Additionally standard deviations (SD) are also shown for the relative recovery percentages.

phenol/chloroform

phenol/chloroform + CTAB

DNeasy Tissue kit

Easy-DNA kit

Magna Pure






EB Dilution

Appr. EB conc. EB/μl

Mean output copies/μl

SD of Mean

% Rel. rec.

SD of % Relative rec.

Mean output copies/μl

SD of Mean

% Rel. rec.

SD of % Relative rec.

Mean output copies/μl

SD of Mean

% Rel. rec.

SD of % Relative rec.

Mean output copies/μl

SD of Mean

% Rel. rec.

SD of % Relative V

Mean output copies/μl

SD of Mean

% Rel. rec.

SD of % Relative rec.


C. pneumoniae EB samples

negative

0

0

0

-

-

0

0

-

-

0

0

-

-

0

0

-

-

0

0

-

-

1.2 × 10-8

0.2

0

0

-

-

0

0

-

-

0

0

-

-

0

0

-

-

0

0

-

-

1.2 × 10-6

20

3.76

4.60

42.8

52.4

1.38

0.410

15.8

4.7

8.36

3.59

95.3

40.9

0.464

0.160

5.3

1.8

8.78

0.005

100

0.06

1.2 × 10-5

200

28.6

29.9

27.0

28.2

38.0

44.7

35.8

42.2

96.2

19.3

90.8

18.2

1.81

1.24

1.7

1.2

106

38.3

100

36.2

1.2 × 10-4

2000

248

208

20.2

17.0

140

60.2

11.4

5.0

982

250

79.8

20.3

18.5

21.7

1.5

1.8

1.23 × 103

331

100

26.9

av rec %

-

-

-

30.0

29.5

-

-

21.0

22.3

-

-

88.6

23.1

-

-

2.8

2.3

-

-

100

20.2

EB spiked aorta tissue samples

negative

0

0

0

-

-

0

0

-

-

0

0

-

-

0

0

-

-

0

0

-

-

1.2 × 10-8

0.2

0

0

0

0

0.219

0.310

18.0

25.4

0

0

0

0

0

0

0

0

1.22

1.72

100

141.3

1.2 × 10-6

20

10.1

3.92

53.2

20.7

14.3

7.05

75.6

37.3

13.9

4.82

73.7

25.5

2.33

0.184

12.3

1.0

18.9

2.86

100

15.1

1.2 × 10-5

200

50.3

24.4

44.5

21.6

125

7.14

110.5

6.3

66.3

30.2

58.7

26.8

29.5

1.11

26.1

1.0

113

0.530

100

0.5

1.2 × 10-4

2000

632

177

49.0

13.7

648

585

50.3

45.3

869

208

67.3

16.2

191

128

14.8

9.9

1.29 × 103

247

100

19.2

av rec %

-

-

-

36.7

26.0

-

-

63.6

43.7

-

-

49.9

34.8

-

-

13.3

10.6

-

-

100

54.2

overall av rec %

-

-

-

33.8

26.7

-

-

45.3

41.2

66.5

35.4

8.8

9.6

100

41.7


Mygind et al. BMC Microbiology 2003 3:19   doi:10.1186/1471-2180-3-19

Open Data