Skip to main content

Table 2 Trace microbial/human 454 FLX library construction

From: Digital PCR provides sensitive and absolute calibration for high throughput sequencing

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

  1. 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.
  2. 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.