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We calculated the expression level of all unigenes from the 24 samples.
We calculated the expression level (RPM) for each replicate separately and compared them to one another.
Instead of taking the derivative of expression level with respect to time, we calculated the expression level derivative with respect to genomic position.
We also calculated the expression level of the DP and SP proteins and our result indicated that there are no significant differences in expression levels between DP and SP proteins for both the datasets (Table 5).
To gain focused information on alternative splicing, we calculated the expression level for each known exon in the human transcriptome relative to the expression of the entire gene, and sub-classified transcripts into those whose general levels or only alternative splicing patterns were modified, thus gaining access to previously unexplored AD-related transcript changes.
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For densitometric analyses, we calculated the expression levels of AR and ERα by dividing these values with that of glyceraldehyde-3-phosphate dehydrogenase (GAPDH), as the internal control.
To obtain the expression differences between sexes, we calculated the expression levels of mixed-sex, male and female adult worms based on both transcriptomic and proteomic analyses.
To begin to understand the dynamics of TEs in A. aegypti we calculated the expression levels of transcripts derived from TEs through development.
However, to allow for qualitative comparison of the model and experimental observations, we calculated the expression levels of a hypothetical ER-dependent gene for four different levels of ER expression (see Figure 7C).
We calculated the expression levels for the four samples of both libraries and then used DESeq2 for normalization, estimation of fold change and mean signal calculation (Supplementary file 2).
We calculated the expression levels of the annotated transcript isoforms using cufflinks v2.1.1 [ 32] with parameters --library-type fr--min-frags-per-transfragve-lengtRNAsrrection --min-frand-per-transfrag 5 and mitochondrialRNAsequencesand mitochondrial sequences.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com