Table 2

Trace microbial/human 454 FLX library construction

Sample ID

Input (ng)

Mean library fragment size (bp)

Input (total molecules by mass)

ssDNA library (total molecules by UT-dPCR)

dPCR replicate CV

Library prep recovery %

Library type

Organism


TS-1

35 ng

500

1.19 × 1011

2.61 × 107

7.07%

0.022%

Shotgun

E. coli

TS-2

25 ng

500

8.52 × 1010

6.15 × 106

8.24%

0.007%

Shotgun

E. coli

TS-3

10 ng

500

3.41 × 1010

4.20 × 106

7.71%

0.013%

Shotgun

E. coli

TS-4

5 ng

500

1.70 × 1010

4.08 × 106

5.65%

0.024%

Shotgun

E. coli

TS-5

1 ng

500

3.41 × 109

4.08 × 105

16.84%

0.012%

Shotgun

E. coli

TS-6

500 pg

500

1.70 × 109

2.31 × 105

5.58%

0.014%

Shotgun

E. coli

TS-7

35 ng

466

1.27 × 1011

2.67 × 107

8.55%

0.023%

Amplicon

E. coli

TS-8

25 ng

466

9.10 × 1010

2.11 × 107

8.50%

0.025%

Amplicon

E. coli

TS-9

10 ng

466

3.64 × 1010

2.15 × 106

4.90%

0.006%

Amplicon

E. coli

TS-10

5 ng

466

1.82 × 1010

8.49 × 105

7.10%

0.005%

Amplicon

E. coli

TS-11

1 ng

466

3.64 × 109

8.67 × 104

21.90%

0.002%

Amplicon

E. coli

TS-12

500 pg

466

1.82 × 109

1.31 × 105

7.60%

0.007%

Amplicon

E. coli

IgG

~1.2 nga

180

1.18 × 1011

3.24 × 106

17.61%

0.003%

Shotgun

M. musclus

K27-1

~1.2 nga

180

1.01 × 1011

1.87 × 106

9.40%

0.002%

Shotgun

M. musclus

K27-2

~1.2 nga

180

8.41 × 1010

1.49 × 106

5.65%

0.002%

Shotgun

M. musclus

Ace

723 ng

550

2.26 × 1012

3.63 × 108

6.10%

0.016%

Shotgun

A. longum

pX

4.9 ngb

180

9.26 × 1010

9.06 × 106

4.60%

0.010%

Shotgun

H. sapien


a DNA samples obtained from chromatin immunoprecipitation (ChIP) experiments. 2000 mouse cells were used for each experiment. The amount of DNA used for 454 library preparation is estimated by assuming 6 pg per cell and ~10% of the genome captured by a typical ChIP experiment. The input for library prep was undetectable by Nanodrop and Agilent Bioanalyzer.

b Quantified by digital PCR using human specific primers at a unique locus, assuming 6.6 pg per cell equivalent. The input for library preparation was undetectable by Nanodrop and Agilent Bioanalyzer.

White et al. BMC Genomics 2009 10:116   doi:10.1186/1471-2164-10-116

Open Data