Global ETD Search
Search theses and dissertations gathered from participating repositories worldwide. Every result links back to the library that holds it. No account is needed.
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Showing 1 to 16 of 16 for “"whole genome bisulfite sequencing"”.
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CHARACTERIZATION OF DNA METHYLATION PATTERNS IN HUMAN EMBRYONIC STEM CELLS AND COLORECTAL CANCER USING WHOLE GENOME BISULFITE SEQUENCING
… resulting in a highly fragmented view of the epigenome. Here, I applied whole genome bisulfite sequencing (WGB-seq) to comprehensively profile undifferentiated human embryonic stem (hES) cell and colon cancer methylome at single base resolution. I will present how an integrative analysis of DNA …
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Investigating the role of epigenetics in rapid adaptation to stress in Arabidopsis thaliana and Sorghum bicolor
… trifloxysulfuron). We analyzed phenotypic and whole-genome bisulfite sequencing data and found that the Arabidopsis phenotype adapts more rapidly to herbicide stress as compared to ecological stresses. DNA methylation changes for glyphosate were minimal after four generations of stress whereas …
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A sequencing-based analyisis of epigenetic modifications of the mitochondrial genome
… mitochondrial DNA (mtDNA) has been studied using whole genome bisulfite sequencing (WGBS), but recent evidence has uncovered major technical issues, which introduce a potential bias during methylation quantification. In this study, we first validate the technical concerns with WGBS using publicly …
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Towards a blood-based biomarker for remyelination: Glial cell death and associated byproducts in demyelinating disease
… by isolating cells from human brain tissue and whole-genome bisulfite-sequencing, resulting in the identification of novel methylation-sensitive ddPCR targets. Next, I completed a thorough, unbiased, sequencing-based tissue/cell-of-origin analysis of plasma from MS and PML patients to …
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ZSCAN4 AND REPLICATION STRESS: SAFEGUARDING GENOME STABILITY IN MOUSE EMBRYONIC STEM CELLS
… of DNA replication is essential for maintaining genome stability. However, replication can be disrupted by both endogenous and exogenous factors, leading to a condition known as replication stress (RS). RS slows down and eventually stalls replication forks. If stalled forks are not resolved, they …
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Targeted Epigenetic Editing to Increase Adult Pancreatic Β-Cell Proliferation
… DNA methylation. I conducted RNA-Seq and whole-genome bisulfite sequencing (WGBS) to profile the aging human β-cell transcriptome and DNA methylome. I found that there are significant changes in gene expression with age, and in DNA methylation, particularly at islet-specific active …
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Variational Mixture Models for non-Gaussian observations: Applications to molecular data
… BeadChip, the EPIC BeadChip and the whole-genome bisulfite sequencing. Each of these DNA profiling platforms quantifies methylation occurrence in different ways, either continuously (rates of methylation intensity) or discretely (counts of methylated reads). Identifying subgroups of …
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Genome-Wide Characterization of the Effects of Nucleic Acid Modifying Enzymes: Cytidine Deaminases and DNA Methylation
… of these cases, the advent of high-throughput sequencing provides methods for genome-wide characterization of AID's effects. This thesis presents the application of a number of genome-scale, sequencing-based methods to characterize the effects of AID deficiency and overexpression on the …
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The Role of DNA Methylation in Defining the Vocal Learning Transcriptome of the Zebra Finch
… DNA methylation. To do so, I performed whole-genome bisulfite sequencing in the RA song nucleus and its adjacent non-vocal motor region. I found that the convergent specialized transcriptome in this nucleus is in part defined by DNA methylation in a subset of these genes. A significant …
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On the Analysis of DNA Methylation
<p>Recent genome-wide studies lend support to the idea that the patterns of DNA methylation are in some way related either causally or as a readout of cell-type specific protein binding. We lay the groundwork for a framework to test whether the pattern of DNA methylation levels in a cell combined …
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The impact of chronic loss of STAG2 on DNA damage repair and the epigenome in acute myeloid leukaemia
… aged 65 and over. Through next generation sequencing studies, the genetic landscape of AML has become increasingly better characterised leading to the identification of recurrent gene mutations. Cohesin complex genes were discovered to be mutated in 13% of AML patients and STAG2 was the …
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Defining the Epigenetic Evolutionary Dynamics that Precede Acute Myeloid Leukaemia
… time, a highly sensitive targeted methylation sequencing strategy was needed. To this end, the first aim of this work was to identify differentially methylated regions (DMRs) in AML. In Chapter 2, we developed a statistical method for identifying DMRs from whole genome bisulfite sequencing data …
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Detection and monitoring of treatment resistance in metastatic cancer through non-invasive DNA methylation-based biomarkers
… strategy combining low-pass (0.5-1X) whole genome bisulfite sequencing (lpWGBS) of plasma DNA with METER, a novel computational tool, designed for low TC scenarios in metastatic setting. Exploiting tumor-type specific DNA-methylation patterns informed from independent tumor tissue …
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The evolution of gene regulatory landscapes in mammalian tissues
… studied. To fill this gap, I analyzed whole-genome bisulfite sequencing (WGBS) and matched chromatin immunoprecipitation assays followed by sequencing (ChIP-seq) of five TFs from the livers of five mammals. I first characterized DNA methylation patterns at transcription factor binding …
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Epigenetic Responses of Arabidopsis to Abiotic Stress
… reproduction. At flowering, DNA for methylation bisulfite sequencing, RNA, and sRNA were extracted from newly formed rosette leaf tissue. Analyzing the individual datasets revealed many differential responses when compared to the untreated control for gene expression, methylation, and sRNA …
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The Effects of Cannabis sativa on the Sperm Epigenome
… the effects of cannabis on the sperm epigenome as use increases across the globe. Further, it is critical to investigate these effects on genes that are uniquely positioned to contribute to early development. The hypothesis of this research was that cannabis exposure is associated with …