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The strand profile in Onychophora differs significantly from L. polyphemus, showing a reversal of strand asymmetry in some regions (fig. 3 B ).
None of the protein-coding genes change their transcriptional polarity in these rearrangements, and so their GC skew values resemble the AAGO strand profile (red and orange bars in fig. 3 A ).
Some genes such as nad5, nad4 and nad4L, and cob do not have a conserved strand profile across the three onychophorans, possibly because of a recent shift in the strand environment of these genes.
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Briefly, COHCOA assumes a two-dimensional background in the raw aligned sequencing data, which arises from two one-dimensional background profiles that are uncorrelated with tethered radical sources: a strand scission profile (leading to horizontal striations) and a reverse transcription-terminating profile (leading to vertical striations).
The single strand DNA profile and quantification was determined by running 1 µl of the samples on the Agilent Bioanalyzer 2100 using a RNA Pico 6000 chip.
These analyses all give the results that the strand bias profile on both sides of the boundary is similar to the original average shown in Figure 2a, and that when an average over all segments is made, transcription gives a only small modification of the pattern – details not shown.
Density profiles from opposite strands were shifted by this value and added together for a unified, strand-independent profile.
An analytical solution for the concentration distribution of mobile strands at intermediate hybridization times provides a convenient tool to calculate the mobile strand concentration profiles.
Sense strand expression profiling was performed according to standard protocol using 250 ng of this RNA.
Sense strand expression profiling was performed according to recommended protocol [ 16].
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