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.
Results
Showing 1 to 20 of 54 for “"bisulfite sequencing"”.
-
Evaluation of Computational and Experimental Parameters in RNA Bisulfite Sequencing Analysis and Applications in Brain Development Studies
… presence of m5C. In this work, we utilize RNA bisulfite sequencing as a transcriptome-wide approach to understand the computational and chemical parameters needed to optimize m5C discovery in the mitochondria and the developing brain. In Chapter 1, we systematically evaluate four preparation …
-
CHARACTERIZATION OF DNA METHYLATION PATTERNS IN HUMAN EMBRYONIC STEM CELLS AND COLORECTAL CANCER USING WHOLE GENOME BISULFITE SEQUENCING
… 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 methylation, gene expression and …
-
The Role of Epigenetics in Hereditary Colorectal Cancer Tumorigenesis: Validation of Genome-Wide Methylation Array Results through Bisulfite Sequencing
… The validation was performed by utilizing direct bisulfite sequencing across 12 selected gene regions on CRC cell lines and histologically normal control samples and comparing the methylation status to the EPIC array results. The genomic regions selected for this analysis were chosen based on …
-
Modulation of RNA Cytosine-5 Methylation by Neuronal Activity and Methyl-donor Folate
… focus on the bioinformatics data analysis of RNA bisulfite sequencing datasets by comparing existing packages with respect to key parameters for alignment and methylation calling and filtering of potentially false positive 5-mrC sites. To investigate the dynamic regulation of 5-mrC modification, …
-
Investigating the role of epigenetics in rapid adaptation to stress in Arabidopsis thaliana and Sorghum bicolor
… 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 the other …
-
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 …
-
A sequencing-based analyisis of epigenetic modifications of the mitochondrial genome
… 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 available …
-
A High-Throughput Approach to Uncover Novel Roles of APOBEC2, a Functional Orphan of the AID/APOBEC Family
… For this thesis, I have combined Next Generation Sequencing (NGS) techniques with state-of-the-art molecular biology to determine the physiological targets of APOBEC2. Using a cell culture muscle differentiation system, and RNA sequencing (RNA-Seq) by polyA capture, I demonstrated that unlike the …
-
Droplet-Based Microfluidics for High-Throughput Single-Cell Omics Profiling
… droplet-based platform to construct single-cell bisulfite sequencing libraries for DNA methylome profiling and allows production of BS library of 2,000-10,000 single cells within 2 d. We applied the technology to separately profile mixed cell lines, mouse brain tissues, and human brain tissues to …
-
Methods and Mechanisms of DNA Methylation in Development and Disease
… Capture Microdissected-Reduced Representation Bisulfite Sequencing (LCM-RRBS), accurately and reproducibly profiles genome-wide methylation of DNA extracted from microdissected fresh frozen or formalin-fixed paraffin-embedded tissue samples. Using this method, I find that significant DNA …
-
Towards a blood-based biomarker for remyelination: Glial cell death and associated byproducts in demyelinating disease
… 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 characterize the …
-
Expression and regulation of genes associated with CNS regeneration and plasticity
… in CNS injury 8 G. Next generation sequencing (NGS) in epigenomic studies 10 H. Aims of this study 11 II. Materials and methods 13 1. Animals and surgical procedures 13 2. In vivo 5-aza and SAM administration 13 3. Primary culture of dissociated adult DRG neurons 14 4. Genomic DNA …
-
Epigenetic Regulation of Nuclear Hormone Receptor DAX-1
… mechanisms. Using gene expression assays and bisulfite sequencing, we have confirmed the relationship between methylation status and DAX-1 expression in MCF7 and A549 cancer cell lines. We have further analyzed the DAX-1 CpG island to observe the presence of epigenetic readers MeCP2 and MBD1 …
-
Molecular mechanisms of acquired gemcitabine resistance in pancreatic cancer
… selection. By RRBS (Reduced Representation Bisulfite Sequencing) analysis, 845 genes were found to have altered methylation. One of these genes, PDGFD, was further investigated and found to have reversible demethylation at its promoter region in the drug resistant cells and contribute to …
-
A photochemical method for the detection of cytosine modifications in DNA
… of covalent DNA modifications; however, bisulfite sequencing, the benchmark technique for the detection of 5-methylcytosine and its oxidised derivatives, is highly destructive and greatly reduces the sequence complexity of DNA samples. These limitations are being addressed through the …
-
The effects of virus-induced maternal inflammation on methylation patterns in skeletal muscle
… from offspring at birth. Reduced representation bisulfite sequencing was used to determine methylation status of individual CpG sites throughout the genome. Differentially methylated CpG sites were used in pathway and gene ontology analysis. Overall frequency of methylated CpG sites was virtually …
-
Integrative Genetic and Epigenetic Studies to Identify Prostate Cancer Genes at Chromosomal 8p
… hypermethylation within these three regions. Bisulfite sequencing verified TNFRSF10C promoter was differentially methylated in 46 out of 59 (78%) tumor samples compared to paired normal samples. And this gene was hemizygously deleted in 44 out of 59 (74.5%) tumors. Methylation and/or deletion …
-
ZSCAN4 AND REPLICATION STRESS: SAFEGUARDING GENOME STABILITY IN MOUSE EMBRYONIC STEM CELLS
… gaps at fork junction. In addition, whole genome bisulfite sequencing revealed that Zscan4 overexpression induces global DNA demethylation in mESC, whereas RS increases global DNA methylation. Finally, short nascent strand sequencing analysis showed that RS leads to increased origin usage, while …
-
Targeted Epigenetic Editing to Increase Adult Pancreatic Β-Cell Proliferation
… 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 enhancers. Further, …
-
Regulation of the Glucocorticoid Receptor Promoter and Its Prognostic Value in Tamoxifen-Treated ER+ Breast Cancer
… biomarker, we developed a targeted multiplex bisulfite sequencing assay to detect promoter methylation in archival tumor samples. With this assay, we evaluated the prognostic and predictive value of GR methylation in ER+ patients from the CCTG MA.12 tamoxifen clinical trial. Region-specific GR …
Page 1 of 3