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The median entropy scores for CpG-island promoters were higher than non-CpG island promoters (HT = 5.19 versus 4.59 Studentt's t-test P-val = 3.1×10−35) (Table S1), indicating that CpG-island promoters had more uniform transcript expression levels.
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Our simulated sequencing process presented each assembly type with difficulties unique to transcriptome reconstruction, such as a non-uniform distribution of transcript expression and the presence of alternative splice forms.
The merged assembly transcripts provide a uniform basis for calculating transcript expression in each condition and the transcript class code.
Transcript expression and differentially expressed genes were analyzed as previously reported (Wu et al., 2015).
Although these two families dominated toxin transcript expression levels in the M. fulvius venom gland, PLA2s did so through uniform expression while 3FTx expression patterns were tremendously biased.
Finally, cuffquant and cuffnorm were used to estimate transcript expression.
Transcript expression was consistently responsive to adipogenic induction across donors.
We also detected decreased EAAT3 transcript expression in schizophrenia and decreased EAAT4 transcript expression in major depressive disorder.
For amplification, 400 ng of the total RNA was used with the Ambion Whole Transcript Expression Kit for Affymetrix GeneChip, Whole Transcript Expression Arrays (Life Technologies Carlsbadd, California).
(c) Comparison of ChIL-seq and ChIP-seq signals with respect to transcript expression ranking.
Accordingly, GPR40 transcript expression was undetectable in BAT and most WAT depots (Supplementary Fig. 3a).
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