For each, the ML tree was estimated and bootstrap support (500 replicates) was estimated using IQPNNI 3.0.1, while LRSH-RELL bootstrap support (1000 replicates) was determined using Treefinder (version: February 2007).
To determine the experimental reproducibility for the time course study, correlation values between replicates of each experiment were determined using Pearson's correlation on the logarithm of the ratio values for every oligonucleotide on the microarray.
PU.1 or Spi-B binding peaks were determined using replicate data from two experiments, sequenced by two independent sequencing core facilities with over 20 million reads per sample.
The mean and standard error were determined using three technical replicates from one representative biological replicate.
Recoveries for the target analytes after extraction were determined using six replicates in three different water matrices shown in Table 4.
Viability and germination percentages were determined, using 10-12 replicates of about 20-40 selected grains.
Size factors for each dataset were calculated to normalize library sizes across replicates, and overall means and variances were determined using a negative binomial distribution model.
Averages and standard deviations were determined using three biological replicates.
All standard errors of divergence distances were determined using 500 bootstrap replicates.
Phylogenetic reconstruction was performed by maximum-likelihood inference using RAxML v7.4.2 (Stamatakis 2006) with a general time reversible model of nucleotide substitution and a GAMMA model of rate heterogeneity, branch support values were determined using 1,000 bootstrap replicates.
