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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.