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 20 of 44 for “"Library preparation"”.
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Reassessing DNA Preservation of Ancient Material from Poulton, UK and Testing and Optimizing of CATS: a Novel Single-Strand DNA Library Preparation Technique
… from Poulton, Cheshire, UK, using standard dsDNA library preparation methods. We targeted cementum of teeth as the optimal substrate for DNA extraction, along with long bones for comparison. A second aim, using a newer single-stranded DNA (ssDNA) library method, namely Capture and Amplification by …
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Droplet-Based Microfluidics for High-Throughput Single-Cell Omics Profiling
… droplets. It has been integrated into various library preparation techniques to accomplish high-throughput scRNA-seq, scDNA-seq, scATAC-seq, scChIP-seq, as well as scMulti-omics-seq. These advanced technologies have been providing unique and novel insights into both normal differentiation and …
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Implementation of global miRNA biomarker discovery in human plasma
… hampered by sequencing bias introduced during library preparation that can result in inaccurate quantification of miRNAs.The first aim of this thesis is to demonstrate the feasibility of routine miRNA profiling in blood plasma by identifying an optimal small RNA-Seq protocol. The second aim is …
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Microfluidic tools for molecular analysis and engineering
… fluidized bed technology. Next, we developed a library preparation system, which reduces the cost of library preparation by 20x and reduces operator pipetting by 100x. Our system uses a droplet based reactor to quickly and reliably prepare sequencing libraries using the lowest amount of DNA to …
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High-throughput Amplicon Sequencing Optimization for Downstream Prediction Purposes
… a genotyping pipeline involving DNA extraction, library preparation with a modified version of a commerical FDP assay, MiSeq FGx sequencing, genotype calling, and quality and ancestry inference assessments. The substantial dataset produced with this project will supply downstream applications in …
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Design, testing, and validation of the search for Extra-Terrestrial Genomes instrument
… acid extraction, sequencer loading, and parts of library preparation. We also experiment with thermal simulations and conduct a sequencing test at Martian conditions, using a custom built thermal vacuum chamber system. Finally, this thesis explores potential avenues for future development and …
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Germline and somatic mutational processes across the Tree of Life
… similarity to double-stranded consensus (duplex) library preparation, can achieve accuracy equal to or greater than duplex reads, which are widely used for ultra-rare somatic mutation detection. To test this hypothesis, I designed and developed himut, a bioinformatics software that leverages the …
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Dynamics of faecal bacterial populations in early infancy as determined by massively parallel sequencing
… increased concentrations of template used during library preparation. Based on diversity measures, meconium specimens harboured the most diverse bacterial profiles. The highest proportions of OTUs classified from meconium belonged to the phylum Proteobacteria (60 %), while the phylum Firmicutes …
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Development of new tools and applications for high-throughput sequencing of microbiomes in environmental or clinical samples
… column-based reaction clean-ups, enabling the library preparation procedure to be performed almost entirely by a robotic liquid handling workstation. Finally, two unique PCR primer systems (primer-clipping and primer-skipping) were engineered to increase the informative read length of 16S …
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Modifikuotų nukleotidų taikymas plataus masto nukleorūgščių analizei /
… within OTDDN were identified. Several known NGS library preparation methods rely on chemoenzymatic approaches, however such techniques suffer from poor efficiency and laborious protocols. In this work modified terminators enabled the integration of fragmentation and sequencing adapter addition …
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The utility of modified nucleotides for high-throughput nucleic acid analysis /
… within OTDDN were identified. Several known NGS library preparation methods rely on chemoenzymatic approaches, however such techniques suffer from poor efficiency and laborious protocols. In this work modified terminators enabled the integration of fragmentation and sequencing adapter addition …
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Elucidating aquatic virioplankton diversity and dynamics using high-throughput DNA sequencing
… careful evaluation of viral isolation and DNA library preparation techniques. Many library preparation strategies employ some form of amplification to obtain sufficient DNA for sequencing. Biases resulting from these techniques may alter interpretations of the occurrence and abundance of viral …
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Description of interactions of Ebola virus with a putative reservoir species using next-generation sequencing
… tool in virology over the past decade as new library preparation techniques have been developed that permit the selective sequencing of small RNAs, and the characterization of entire viral populations at incredible levels of detail. For this work, I exploited this technology to explore two …
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A Test of Rad Capture Sequencing on Ethanol-Preserved Centennial and Contemporary Specimens of Philippine Fishes
… DNA for simultaneous comparison. Two DNA library preparation methods, single digest RADseq (“un-baited” sequences) and Rapture or capture probes designed from the initial RADseq tags (“baited” sequences), and two filtering pipelines, dDocentHPC and ANGSD are tested using four fishes with …
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Viengrandines mažąsias RNR modifikuojančių gyvūnų Hen1 metiltransferazių taikymas RNR žymėjimui ir sekoskaitai /
… and RNA sequencing), the method for the cDNA library preparation for single-stranded RNA sequencing. With mDOT-seq in hand we have not only demonstrated that it can be applied for the sequencing of small eukaryotic RNAs (such as microRNA or siRNA), but also for the first time characterized the …
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Evolutionary Dynamics of Brown Treesnake (Boiga irregularis) Reproductive Ecology, with Implications for Invasive Species Control
… digest restriction-site associated DNA (ddRAD) library preparation to reconstruct a 15-year multi-generational pedigree of BTS in an experimentally-closed population (N = 426). When juxtaposed with ecological data, the pedigree served to: (1) Characterize fundamental aspects of BTS reproductive …
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The genomic characterization of carbapenemase-producing Serratia marcescens at a tertiary hospital in South Africa
… using Illumina MiSeq, with the Nextera DNA Flex Library Preparation Kit. Sequence data was analysed in-house using srst2 and Tychus, and CRSM and control isolates were compared. Results Twenty-one CRSM and four control isolates were sequenced and analysed. Twenty-four different resistance genes …
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Detecting tumour signals from multi-modal biological features of cell-free DNA fragments
… depends on instrumental processes such as library preparation and feature extraction. First, I used sWGS data of ten different healthy donors using six library kits and ten data processing routes. Variations across different conditions were evaluated. I collected 430 healthy plasma samples …
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RACE-Seq identifies the Argonaute-2 cleavage products of RNA interference-based oligonucleotides
… loop. The project also focused on optimising the library preparation, data filtering and data presentation for RACE-Seq. A simplified, low computation data analysis pipeline was designed and used to align the filtered dataset to a reference sequence and to count the 5’ ends. RACE-Seq is presented …
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Improving the applicability of metabarcoding to monitor salmon farming impacts on benthic environments
… and contextualising two sources of variation in library preparation; (ii) identifying metabarcoding-inferred indicators associated with benthic macrofauna and sediment sulphide concentrations; and (iii) investigating bacterial function associated with farm impact. Both the DNA extraction kits and …
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