Characteristics of tissue-specific editomes in zebrafish. A Number of (commonly) edited sites of a single tissue or sites common to two or more tissues. This graphical UpSetR plot visualizes intersections of RNA editing sets in which the rows of the matrix represent the sets of tissues and columns represent their intersections (shared RNA editing behavior). Black filled circles indicate intersections; light gray circles indicate no intersection. The sizes of the intersections are shown by the bar graph above the matrix. B The per Mb density of edited sites for each tissue. Data are shown as the mean ± SD, n = 3. C Editing level at the detected edited sites in each tissue. Editing level was estimated as the number of G/the number of (G + A) in each editing site, in which G is the edited base count and A is the reference allele count. The shaded areas represent the distribution of editing levels. The horizonal lines in the boxes represent the median value of editing levels. D, E Overall editing levels of sites detected in each tissue of whole genome (D), and non-repeat DNA regions or repeat DNA regions (E) sites in various zebrafish tissues. Overall editing level is defined as the percentage of edited nucleotides at all known editing sites and was estimated as the total number of G in all editing sites/the total number of (A + G) in all editing sites. Statistical significance between brain and ovary for “Number of A-to-G RNA editing sites per Mb” and “Overall editing level of sites detected in each tissue (%)” were calculated using an unpaired t-test. n = 3, ns, not significant, *P < 0.05, **P < 0.01
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