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Fig. 3 | Genome Biology

Fig. 3

From: Using protein-per-mRNA differences among human tissues in codon optimization

Fig. 3

CUSTOM generates fluorescent variants with desired tissue-specific expression. A Selected eGFP and mCherry sequences optimized to lung and kidney using CUSTOM. The color code corresponds to the optimality ratios of Fig. 2B. B Using these sequences, we designed four of constructs by placing a mCherry and an eGFP with opposite tissue-specificity under an inducible bidirectional promoter. C Ratios of eGFP and mCherry for each of the four constructs in A549 and HEK293T cell lines, detected by flow cytometry. Three biological replicates are downsampled to 1000 cells per group and summed; see individual replicates in Additional file 1: Fig. S7E. On the right, the distribution of all four constructs together are shown. D Conceptual summary of the relationship between the gene codon usage and their expression across tissues. E Ratios of eGFP and mCherry for each of the four constructs in primary cells, detected by flow cytometry. Top and bottom panels correspond to two independent batches of primary cells (see the “Methods” section). The number of cells within each group is specified. Center values represent the median. Statistical differences were determined by two-tailed Wilcoxon rank-sum test and are denoted as follows: *p ≤ 0.05, **p ≤ 0.01, ***p ≤ 0.001, ****p ≤ 0.0001

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