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SAGE software excludes replicate ditags from the tag sequence catalog because the probability of any two tags being coupled in the same ditag is small, even for abundant transcripts.
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Cytotypes were obtained by excluding replicated counts (i.e. the same chromosome number for the same taxon).
After excluding replicate isolates, four independent strains with the longer allele remained.
Excluding replicate tissues from the same major organ, we identified genes exclusively expressed in the leaf, shoot, root, shoot tip and stem.
Custom software called SeeGH was used to combine replicates and visualise all data as log2 ratio plots in SeeGH karyograms and exclude replicate data points which exceeded a standard deviation of 0.075 (Chi et al, 2004).
Results from the statistical analysis of the full data set, that is without excluding replicates with mortality in the controls, were qualitatively similar to those presented below (data not shown).
After excluding 186 replicates the final matrix used for analyses contained 192 individuals and 792 fragments.
To calculate the fraction of replicated DNA, the S∶G1 ratios were distributed over 62 bins of equal width (excluding sex chromosomes, which replicate late in this cell line).
The excluded samples essentially represent replicate sample types for many genes that would hinder the correct determination of maximum and minimum spline values, confounding the ordering or grouping of genes in context of the life cycle.
One SNP per locus was chosen and, after accounting for multiple testing, SNPs with power to replicate <80% were excluded.
After further analysis to exclude the replicate identifications, the final identification of 3 down-regulated and 23 up-regulated proteins were allowed.
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