Tissue specific transcriptome of zebrafish in ache mutant embryos

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buir.advisorKarakayalı, Özlen Konu
dc.contributor.authorDinçaslan, Fatma Betül
dc.date.accessioned2019-07-01T07:44:17Z
dc.date.available2019-07-01T07:44:17Z
dc.date.copyright2019-06
dc.date.issued2019-06
dc.date.submitted2019-06-28
dc.departmentDepartment of Molecular Biology and Geneticsen_US
dc.descriptionCataloged from PDF version of article.en_US
dc.descriptionThesis (M.S.): Bilkent University, Department of Molecular Biology and Genetics, İhsan Doğramacı Bilkent University, 2019.en_US
dc.descriptionIncludes bibliographical references (leaves 138-149).en_US
dc.description.abstractDifferential 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.en_US
dc.description.degreeM.S.en_US
dc.description.statementofresponsibilityby Fatma Betül Dinçaslanen_US
dc.embargo.release2019-12-28
dc.format.extentxix, 149 leaves : illustrations (some color), charts (some color) ; 30 cm.en_US
dc.identifier.itemidB156252
dc.identifier.urihttp://hdl.handle.net/11693/52082
dc.language.isoEnglishen_US
dc.publisherBilkent Universityen_US
dc.rightsinfo:eu-repo/semantics/openAccessen_US
dc.subjectTissue specificityen_US
dc.subjectAche mutantsen_US
dc.subjectDifferential gene expressionen_US
dc.subjectTau metricen_US
dc.subjectZebrafishen_US
dc.subjectAcetylcholinesteraseen_US
dc.subjectLighten_US
dc.subjectEmbryosen_US
dc.subjectTsien_US
dc.subjectHgen_US
dc.subjectSpmen_US
dc.subjectGinien_US
dc.subjectRPKMen_US
dc.subjectSequencing depthen_US
dc.subjectTPMen_US
dc.subjectDarken_US
dc.titleTissue specific transcriptome of zebrafish in ache mutant embryosen_US
dc.title.alternativeAche mutasyonlu zebrabalığı yavrularında dokuya özgü transkriptomuen_US
dc.typeThesisen_US

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Dept. of Molecular Biology and Genetics - Master's degree