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Third, the number of blood samples for input function used for integration plot analysis can be a factor that causes different results in calculated transfer rates.
JH and HR developed the samples for input to the sequencing core for RNA-Seq analysis.
However, one MDA DNA sample (for inputs of 1 ng and 0.1 ng) revealed a genotype discordant with the controls, and 36 MDA DNA samples (for input of 0.01 ng) gave results dissimilar to the sequenced controls.
The resulting chromatin was centrifuged at 15,000× g for 10 min and the resulting supernatant was aliquoted in 200 μl samples for immunoprecipitation and 25 μl samples for input.
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For both R. socialis and R. magnacalcarata, a pair of RNA samples were combined and further purified using ethanol sodium acetate precipitation, to produce a more concentrated sample for input into the cDNA synthesis reaction.
Conventional direct sampling methods for input uncertainty propagation, such as Monte Carlo sampling or Latin Hypercube sampling, require a very large number of samples for convergence of the statistical parameters, such as mean and standard deviation, and can be prohibitively time-consuming.
We selected a random subset consisting of 70% of the samples (~500,000 samples) for model input and used the remaining 30% for model evaluation and validation.
Sample files for input data are available on the "Download" page.
Following centrifugation (4000 g at 4°C for 5 min), the supernatants were retained and a sample reserved for input DNA.
We run 10,000 Monte-Carlo simulations of the model employing Latin Hypercube sampling [ 29], using the @Risk software package (Palisade, Newfield, NY, USA; version 4.05); our model is constructed to consistently sample values for input variables from the data from the same year at each iteration.
The rest of the samples were kept for INPUT.
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