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From each type, the strain with the highest transcript rate was chosen for further characterization (Figure 1).
The cumulative value of transcript rate was used to compare expression profiles of tested SSH clones and to evaluate their possible impact on plant-pathogen interaction.
In order to compare the possible impact of the expression of each analyzed gene on host-plant interaction the cumulative value of transcript rate (CVTR) was used as described previously [ 11].
Timing of the TI with the highest category score: If a TI with a higher category score than the category of the ITI is identified later in the transcript, rate it's timing on items 13 and 14.
The cumulative value of transcript rate (CVTR) was introduced to compare expression profiles of tested SSH clones and to evaluate their possible impact on plant-pathogen interaction in a particular line.
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Data on mouse transcriptional rate, transcript abundance, transcript half-life, translational rate, protein abundance and protein half-life was obtained from Schwanhausser et al.
Information on mRNA abundance, transcriptional rate, transcript half-life, histone modifications, transcripts bound to RNA binding proteins, 5′UTR length, RNA secondary structure, and codon bias for S. cerevisiae was obtained from Holstege et al.
As previously reported, a great variability in transcript rates was observed for both unchallenged and immune challenged (Vibrio or SSW) oysters.
Positive associations in this analysis are most likely to result from direct allele-specific effects on transcription rate or transcript stability.
The reproducibility of triplicate array analyses was high with a mean coefficient of variation (CV) ranging from 0.12 to 0.14 for transcripts rated as present or marginal.
Transcription can be measured in a bulk culture by examination of the location of RNA polymerase using ChIP, the strand-specific NET-seq (Churchman and Weissman 2011), or an equivalent method, but these methods have the drawback that polymerase density reflects both the transcript initiation rate and the rate of polymerase elongation.
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