Dinçaslan, Fatma Betül2019-07-012019-07-012019-062019-062019-06-28http://hdl.handle.net/11693/52082Cataloged from PDF version of article.Thesis (M.S.): Bilkent University, Department of Molecular Biology and Genetics, İhsan Doğramacı Bilkent University, 2019.Includes bibliographical references (leaves 138-149).Differential expression of specific genes in certain tissues provides information about tissue specificity which might define phenotypes of various tissues. It is possible to understand the tissue-specific effects of knockout or knockdown studies performed on zebrafish embryos, using such genes. In this study, publicly available RNA-seq datasets providing data on 15 of the tissues from 5-9 months old zebrafish were used to estimate tissue specificity for zebrafish genes. Three different normalizations (i.e SD, RPKM, TPM) of 15 tissues were performed to compare; and the results were used to understand whether a given zebrafish mutant has significant enrichments for tissue-specific genes, based on different metrics including Tau, TSI, Hg, Spm, Gini, Counts. Application of these pipelines to the publicly available acetylcholinesterase (ache) mutant vs. healthy zebrafish data (GSE74202) revealed that many retina- muscle-, and liver-specific genes were downregulated in ache mutants. The downregulation of retina and liver specific genes (such as arr3a, rpe65a, rom1b and fabp10a, respectively) were futher confirmed with qPCR on comparative study of ache (+/?) and ache (-/-) 3 days post fertilization (dpf) zebrafish embryos. In addition a pilot experiment testing the effects of constant light and constant dark exposure for 3-5 dpf ache mutant and healthy embryos were performed, suggesting that the expression of retina-specific genes were more prominently affected in 3 dpf mutant embryos regardless of light.xix, 149 leaves : illustrations (some color), charts (some color) ; 30 cm.Englishinfo:eu-repo/semantics/openAccessTissue specificityAche mutantsDifferential gene expressionTau metricZebrafishAcetylcholinesteraseLightEmbryosTsiHgSpmGiniRPKMSequencing depthTPMDarkThesisB156252