Paliy Lab
Diggs Laboratory for Life Science Research : Department of Biochemistry and Molecular Biology : Wright State University

O. Paliy and B. Foy

Mathematical modeling of 16S ribosomal DNA amplification reveals optimal conditions for the interrogation of complex microbial communities with phylogenetic microarrays (2011) Bioinformatics, 27(15): 2134-40.

Full text (pdf)

Supplementary material:

  • Supplementary figure S1 (png): Agarose gel electrophoresis of gDNA samples amplified with different number of PCR cycles

  • Supplementary figure S2 (png): Simulation results - average sample amplification rate vs PCR cycle number

  • Supplementary figure S3 (png): Simulation results - fraction of 16S rDNA in amplified sample vs PCR cycle number

  • Supplementary figure S4 (png): Simulation results - deviation of relative 16S rDNA abundances with PCR cycle number [graphs are shown for most abundant gDNA species in the original sample {rank 1}, mid-abundant {rank 200}, and least abundant {rank 400}]

  • Supplementary figure S5 (png): Simulation results - yield of PCR reaction as a function of PCR cycle number and amount of starting gDNA [no loss due to PCR reaction purification is assumed]

  • Supplementary figure S6 (png): Simulation results - number of PCR-amplified samples needed to becombined to obtain 1500 bp microarray load [we assume 50% loss of DNA during PCR purification]

  • Supplementary table S1 (pdf): Comparison of simulated and experimental results

  • Detailed model description (pdf)

  • Matlab files used to run simulation (zip)

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Department of Biochemistry and Molecular Biology
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Wright State University
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