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 36 for “"paired end"”.
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Evaluation and annotation of Bemisia tabaci transcriptome data using paired-end RNA sequencing
Bemisia tabaci (B. tabaci), a major crop pest of important food security crops, transmits more than 100 plant viruses. Despite its global importance as one of the world’s top 100 invasive species, limited genomic resources are available in public domains. In this study, transcriptomic datasets from …
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Computational Pipeline for Human Transcriptome Quantification Using RNA-seq Data
… format and is compatible with both single-end and paired-end sequencing technologies. It also allows researchers to accurately calculate gene expression abundance scores.</p> </p>
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Transcriptiome analysis of a migraine model
… the Illumina HiSeq 4000 platform to produce paired end reads of 100 bp. Opalin, Slc32a, Cacna1b, and H2-Eb2 were among the 110 genes exhibiting significant interaction effects. The 165 genes presenting different expression patterns between the treatment and control groups included Aldh1a1 and …
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The structure and evolution of breast cancer genomes
… molecular cytogenetics and massively parallel paired end sequencing. I then used these structural genomic maps to predict fusion transcripts and demonstrated expression of five fusion transcripts in HCC1187, three in VP229 and four in VP267. Even though chromosome aberrations disrupt and fuse …
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Estudio comparativo de herramientas bioinformáticas para el análisis metagenómico sobre el microbioma humano
… de Illumina, llevando a cabo una secuenciación paired-end. El análisis bioinformático se realizó con tres de los softwares más utilizados en la actualidad, que son: Gaia, Qiime2 y Mothur. Estos dos últimos son de código abierto por lo que para llevarlos a cabo se hizo uso de una máquina virtual …
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A GPU program to compute SNP-SNP interactions in genome-wide association studies
… of human genome are made more accessible. Paired end sequencing of short reads is currently the most sensitive method for detecting somatic mutations that arise during tumor development. In this study, a novel approach to optimize the detection of structural variants using a new short read …
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Genetic basis of human disorders of gonadal development
… kit, sequencing was accomplished using paired-end sequencing technology on an Illumina HiSeq2000 sequencer. The data from the Illumina sequencers was analyzed first using the Illumina sequencing data analysis pipeline for quality control. Paired end reads were aligned to the Human …
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De novo Sequencing and Analysis of <em>Salvia hispanica</em> Transcriptome and Identification of Genes Involved in the Biosynthesis of Secondary Metabolites
… we generated 90 million high quality 150 bp paired-end sequences from the chia leaf and root tissues. The sequences were de novo assembled into 103,367 contigs with average length of 1,445 bp. The resulted assembly represented 92.2% transcriptome completeness. Around 69% of the assembled …
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Empirical accuracy bounds for next-generation sequencing variant calling workflows
… of read length. Additionally, we will show that paired-end sequencing with large insert sizes (also referred to as ""mate-pair"" sequencing) is capable of mapping >99% of the human genome. We have developed a set of tools, NEAT (Next-generation Error Analysis Toolkit), which we use to create …
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Genome reconstruction and combinatoric analyses of rearrangement evolution
… evolution consistent with read coverage and paired end data, giving insights on the possible molecular mechanisms underlying rearrangements. Looking at the combinatorics of both tandem and inverted duplication, we developed an algebraic formalism for the representation of these processes. …
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Construction and analysis of the miscanthus genespace
… sequenced at high depth as 100x75 bp paired-end reads. Chapter 1 reports the sequence capture of a doubled haploid Miscanthus sinensis plant and its parent, and chapter 2 reports the sequence capture of energy cane and two other Miscanthus species. This sequence capture design was able …
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Metagenomic Analysis of Antibiotic Resistance Genes in the Fecal Microbiome Following Therapeutic and Prophylactic Antibiotic Administration in Dairy Cows
… subjected to DNA extraction followed by Illumina paired-end HiSeq sequencing and quantitative polymerase chain reaction (qPCR). Illumina sequences were analyzed using MG-RAST and the Antibiotic Resistance Gene Database (ARDB) via BLAST. Abundance of ampC, ermB, tetO, tetW, and 16S rRNA genes were …
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Development of Genomic Resources for the Evaluation of Red Snapper, an Emerging Species Candidate for Marine Aquaculture and Stock Enhancement
… were developed through screening of Illumina paired-end sequencing reads. Microsatellite loci and Single Nucleotide Polymorphisms (SNPs) generated through Restriction Site Associated DNA (RAD) sequencing were assayed in 5 outbred full-sib families to construct a high-density linkage map of the …
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Xenobiotic detoxification in the navel orangeworm Amyelois transitella (Lepidoptera: Pyralidae)
… of the caterpillar. A total of 319 million paired-end reads were sequenced from larval midgut tissue, and these were assembled de novo into 186,000 contigs. Identification of putative P450s in this assembly was carried out using BLAST homology. As detoxification of phytochemicals, …
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Influence of landscape-variation in geochemistry on taxonomic and functional composition of microbial mat communities in the McMurdo Dry Valleys, Antarctica
… sequenced on an Illumina NextSeq500 in a 150 bp paired end format. Raw sequences were uploaded to the MG-RAST server for processing and annotation. Community taxonomic and functional annotation were determined using the RefSeq and SEED Subsystem databases, respectively. The results revealed …
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De novo sequencing, assembly and analysis of the genome and transcriptome of the nematode Panagrolaimus superbus
… Panagrolaimus superbus can survive for extended peri- ods of time in a desiccated state (anhydrobiosis) and is also freezing tol- erant (cryobiotic). These adaptations make it an interesting candidate for genome and transcriptome sequencing using second generation high through- put methods. …
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De novo assembly of transcriptome and genome data from the Asia I mtCOI genetic clade of Bemisia tabaci
… through de novo assembly of 206 million 250 bp paired-end reads generated on the Illumina MiSeq 2500 platform using Platanus. They were found to encode 41,981 PCGs and also contained 990 ncRNAs and repetitive elements (45.66%). A selection of 741 full-length genes were studied and found to …
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Assessing Arbuscular Mycorrhizal Fungal community composition and diversity across a land-use gradient in Eastern Washington prairies
… on the Illumina MiSeq platform using 300bp paired-end sequencing. Sequences were quality filtered and grouped into amplicon sequence variants (ASVs) using QIIME2. Taxonomy for the recovered AMF lineages was assigned using the MaarjAM database. Our results suggest that the community …
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Molecular display of synthetic oligonucleotide libraries and their analysis with high throughput DNA sequencing
… four rounds of antigen selections by multiplex paired-end Illumina sequencing. The HMM library generated multiple antibodies against an emerging cancer antigen and is the basis of a next generation antibody production platform. In a second application of these technologies, we have created a …
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Noxious Cellular Injury Triggers an Oxidative Stress Gene Response
… assembled and annotated utilizing the Illumina paired-end RNA-seq approach with software packages HISAT2 and StringTie. Results showed 243 genes were differentially expressed (106 upregulated, 137 downregulated) between CA venom stimulated and non-stimulated cells (p<0.05). HEK-293T stimulated …
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