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The widening of the hook by –log d reflects the decrease of the mean transcript concentration due to incomplete amplification and degradation.
The mean transcript concentration averaged over all probes can be estimated as the geometric mean over the 3′ and 5′ transcript concentrations, (23) s chip ≈ s 3 ′ 10 − 1 2 Δ γ 3 ′ / 5 ′ ≈ s 3 ′ · s 5 ′ s 3 ′ ≈ s 3 ′ · s 5 ′ if one assumes uniformly distributed probes along the relevant transcript regions.
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Throughout this paper, the genes targeted by transcript probes are called "T-genes", which means "transcript-level genes".
While our method yielded excellent predictions of absolute transcript concentration, we did not predict concentration for all transcripts in the low concentration category (Fig. 1 and 2).
We assume that there is a direct correlation between mRNA transcript concentration and the concentration of the morphogen protein.
In doing so, we can model the concentration of the morphogen's mRNA transcripts in the system and equate the corresponding mRNA transcript concentration profile to that of the morphogen protein concentration profile.
The mean transcript length is 564 nucleotides.
The mean transcript length, maximum transcript length, and N50 size of Trinity transcripts were 1112, 22,887, and 1863, respectively.
(B ) Mean transcript lengths were calculated from two independent experiments.
(B ) Mean transcript lengths were averaged from two independent experiments.
This analysis shows that degradation can reduce the transcript concentration to less than one third of the initial transcript abundance.
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