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 19 of 19 for “"sequencing depth"”.
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Assembling improved gene annotations in Clostridium acetobutylicum with RNA sequencing
… integrating bioinformatic predictions with RNA sequencing(RNA-seq) data. Samples were acquired under butanol, butyrate, and unstressed treatments across various growth stages to sample the transcriptome from a range of physiologically relevant conditions. Analysis of an initial assembly revealed …
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Rna-Sequencing Applications: Gene Expression Quantification and Methylator Phenotype Identification
<p>My dissertation focuses on two aspects of RNA sequencing technology. The first is the methodology for modeling the overdispersion inherent in RNA-seq data for differential expression analysis. This aspect is addressed in three sections. The second aspect is the application of RNA-seq data to …
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Population Structure of Lake Whitefish (Coregonus Clupeaformis) on Multiple Spatial Scales: Transitioning to a Genomics Approach
… molecular ecologists are transitioning to direct sequencing of thousands of single nucleotide polymorphisms in a subset of the genome based on reduced representation DNA libraries (RRL). These tools better represent evolutionary processes on a genomic level but molecular ecologists are now faced …
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CRISPRi screens to identify combination therapies for the improved treatment of ovarian cancer
… for knockdown efficiencies and variances in sequencing depth.
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The design and statistical analysis of single-cell RNA-sequencing experiments
<p>Next-generation DNA- and RNA-sequencing (RNA-seq) technologies have expanded rapidly in both throughput and accuracy within the last decade. The momentum continues as emerging techniques become increasingly capable of profiling molecular content at the level of individual cells. One goal of this …
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RNA-sequence analysis of human melanoma cells
RNA-sequencing refers to the use of high throughput sequencing technologies that are used to sequence cDNA in order to get the complete information of a sample's RNA content. The objective of this study is to analyze this data in different aspects and to characterize gene expression. Besides this …
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Investigation of HPV16-related genomic alterations in cervical squamous cell carcinoma
… raw count data, accounting for differences in sequencing depth and RNA composition between samples. A negative binomial distribution model was fitted to the normalized count data for each gene. Statistically significant genes were filtered to an adjusted p-value <= 0.05 and log2 fold change >= …
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Leveraging Single-Cell ATAC-Seq for Genomic Language Models and Multimodal Foundation Models
… Assay for Transposase-Accessible Chromatin using sequencing (scATAC-seq) has emerged as a powerful tool for profiling chromatin accessibility at single-cell resolution. By capturing epigenomic landscapes, scATAC-seq provides critical insights into the regulatory elements that govern gene …
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A Novel NGS Assay to Detect Any KMT2A Fusion Transcript at Low Levels
… these various fusions. Standard next-generation sequencing (NGS) methods cannot accurately detect genetic alterations at low frequencies because of inherent technical errors and the need for high sequencing depth. Blocker Displacement Amplification (BDA) technology enables selective detection of …
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Expression and function of small RNAs in normal and psoriatic skin
… small RNAs in human skin with Next Generation sequencing, and detected known miRNAs, variants of known miRNAs, and novel miRNAs with unprecedented sequencing depth. Eighty known and 18 novel miRNAs were two- to 42-fold differentially expressed in psoriatic skin. Computational and experimental …
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Integrating -Omics For Studying Functional Role Of Ulcerative Colitis Risk Associated Loci.
… financial reasons we failed to reach the target sequencing depth for both ATAC seq and RNA seq experiments. In addition, when combined with very low participant numbers, our data sets were not strong enough to reliably identify the functional role of GWAS variants. However, for practice, we …
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Next-generation sequencing (NGS) for human disease research
차세대 염기 서열 분석법(Next-generation sequencing)은 DNA 유전 정보를 읽어내는 기술을 자동화한 1세대 생어(Sanger) 방식에서 대량의 병렬 데이터 생산이 가능하게 진화한 차세대 염기 서열 분석기가 생산한 데이터를 분석하는 기법을 의미한다. 2007년, 차세대 염기 서열 분석법의 등장은 무어의 법칙(Moore's law)을 능가하는 속도로 염기 서열 분석 비용을 감속시키고 있으며 곧 한 사람의 염기 서열 분석이 $1,000에 가능하게 되리라는 것이 명확해졌다. 차세대 염기 서열 분석법은 정착 단계를 …
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Role of Retrotransposons as a Major Source of Intra- and Inter-Individual Epigenetic Variations in the Mammalian Genome
… targeted repeat element bisulfite sequencing (HT-TREBS) technique. We obtained CpG methylation data of 5135 loci of five IAPLTR subtypes in three different tissues of four 1-week-old mouse littermates. An average of 52,000 CpG positions per sample with average sequencing depth of …
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Harnessing CRISPR-Cas9 screens to identify functional genetic interactions
… appropriate guide-RNA representation, sufficient sequencing depth, and the use of multiple high-editing clones. Careful consideration of these factors in screen design and execution allows successful CRISPR-Cas9 screens to be carried out in both p53-proficient and p53-deficient cells, thereby …
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Population Sequencing for Studying Natural and Artifcial Variation in C. elegans
<p>The advent of high coverage and low cost sequencing technologies has allowed for</p><p>newer and more powerful approaches in molecular and population genetics. Transposon</p><p>sequencing, where genome-saturated mutant populations allele frequencies are</p><p>measured before and after selection, …
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Statistical power for RNA-seq data to detect two epigenetic phenomena
… using ultra high throughput next generation sequencing technologies. Using RNA-seq, a genome-wide study can investigate genome-wide genomic imprinting and AEI without prior knowledge of genes or coding regions. Moreover, RNA-seq shows many benefits compared with traditional microarray …
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Leveraging community-based sequencing approaches to characterise the dairy microbiome
… microorganisms, advances in high-throughput DNA sequencing have enabled the study of entire microbial communities in food or food-related samples. In this thesis, shotgun metagenomic sequencing was employed to investigate microbial communities in bulk tank milk. First, shotgun sequencing was used …
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Investigating the Genomics and Heterogeneity of Childhood Non-Hodgkin Lymphoma
… mice was demonstrated through whole genome sequencing (WES). In addition, pervasive genetic ITH across time and space was detected by multiregion WES of BL cases, meaning that single biopsies cannot rule out the presence of a given variant, regardless of sequencing depth. Furthermore, …
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Correlates of tuberculosis and non-tuberculosis morbidity and immunity in sub-Saharan African HIV-exposed, uninfected infants
… and 16S ribosomal ribonucleic acid (rRNA) gene sequencing was performed. Plasma IgG anti-tetanus antibody titers were measured by enzyme-linked immunosorbent assay (ELISA). The effect of HIV exposure on infant gut microbiota composition was relatively modest compared to the impact of age and …