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Fibrin gels of days 7 and 28 were processed for qPCR and culture supernatants were collected and frozen at -80°C until usage for analysis of cytokines, bFGF and GAG.
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For statistical analysis of APA shifts, genes with at least two PACs (TPM > 3) were selected for analysis of differential usage.
CodonW [ 74] was used for analysis of total codon usage.
For analysis of differential exon usage between spermatogenic and oogenic gonads, we used the DEXSeq package for R/Bioconductor (Anders et al. 2012).
Until now, besides the usage of GenoTubes Livestock for DNA analysis of the tested individuals, only a few studies described the use of GenoTubes for detection of infectious agents in animals [ 14, 15].
5) Perhaps more description of the TIE*method would be helpful The point-by-point response follows: 1) The revised manuscript contains expanded literature review about usage of multivariate methods for predictive analysis of SNP data.
Examples are used to demonstrate the usage of the graph model for analysis and evaluation of a gear transmission chain.
In particular, dimensionality reduction methods have widely been used for the analysis of codon usage patterns in microbial genomes.
For the analysis of codon usage tables we developed a special similarity measure which has been derived from the well-known chi-square test for the comparison of two distributions.
> -wrap-foot> For codon usage bias analysis, the values of expected effective number of codons (ENC or Nc) from GC content at synonymous third codon position (GC3s) under H0 (null hypothesis, i.e., no selection) were calculated according to the equation of Wright (1990): Nc = 2 + S + {29/[S2 + (1 − S ]} (S denotes GC3s).
Of the four CA methods, WCA was found to be most useful for the analysis of synonymous codon usage.
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