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 “"Transcriptome Assembly"”.
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Assembling improved gene annotations in Clostridium acetobutylicum with RNA sequencing
… across various growth stages to sample the transcriptome from a range of physiologically relevant conditions. Analysis of an initial assembly revealed errors due to technical and biological background signals, challenges with few solutions. Hurdles for RNA-seq transcriptome mapping research …
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De novo sequencing, assembly and analysis of the genome and transcriptome of the nematode Panagrolaimus superbus
… make it an interesting candidate for genome and transcriptome sequencing using second generation high through- put methods. In this project the transcriptome of P. superbus was sequenced using the 454 (Roche) platform. To enrich for stress-related genes, nema- todes were exposed to one of the …
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Integrating bioinformatic approaches to promote crop resilience
… learning approach to determine factors impacting transcriptome assembly and quantitatively evaluate transcriptome completeness, 2) dissect complex physiological pathway interactions in Solanum pimpinellifolium under combined stresses—using comparative transcriptomics, and 3) develop a genome …
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A DE NOVO COMPUTATIONAL DISCOVERY PLATFORM FROM RNA TO PROTEIN
… remains vastly unexplored. Moreover, the transcriptome composition changes in different human cell types, tissues, and conditions. Therefore, there is great need for unbiased, dataset-specific annotation efforts. In this regard, transcriptomic and proteomic methods can help elucidate …
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Characterization of the transcriptome and the peptidase and the non-peptidase homologs of callosobruchus maculatus
… homologs were annotated. Here a de novo transcriptome assembly was built from 840,766 Roche 454 reads using CLC Genomics workbench. The assembly resulted in 35,111 contigs that were analyzed using Blast2GO. Important not only in digestion, but in other functions such as immune response …
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Transcriptional regulation of seasonal desiccation tolerance in the fronds and rhizome of the fern Anemia caffrorum
… to conduct short- and long-read sequencing for transcriptome assembly and gene expression studies. Transcriptome assembly using long read data outperformed de novo short read assembly as it resulted in greater rates of annotation and yielded a less fragmented assembly. The transcriptome was …
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Genomic evidence of long-term asexuality at the northern range limit of wetland plant, Decodon verticillatus (Lythraceae)
… at its northern range limit. I did a de novo transcriptome assembly and compared SNPs in sexual and asexual populations at and approaching the northern range limit to determine if range-edge, asexual populations show genomic signatures of long-term asexuality consistent with the AEH. Asexual …
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Automated, highly scalable RNA-seq analysis
… analysis framework for performing differential transcriptome expression, transcriptome assembly, variant and RNA-editing calling. It handles the entire stack of an analysis, from downloading and installing hundreds of tools, libraries and genomes to running an analysis that is able to be scaled …
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New Targets of p53 Regulation: From Aging to Immune Response
… sequencing data called Annotation Independent Transcriptome Assembly. Using this approach to interrogate the transcriptome of p53+/+ and p53-/- mouse embryonic fibroblasts (MEFs), I identified Mmergln-int among the top genomic loci differentially expressed between p53+/+ and p53 -/- cells. …
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Genomic approaches to understand sweetpotato root development in relation to abiotic factors
… Tags was done to generate a genome-wide transcriptome assembly. About 33 million sequences were assembled into 77,663 unigenes; 52,322 (69.55%) of these unigenes matched to a protein sequence from UniprotKB. Data from de novo root transcriptome enriched the existing sweetpotato gene index …
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Reproductive plasticity and the evolution of the insect societies
… accommodation. In Chapter 3, I present a de novo transcriptome assembly for Megalopta genalis, a facultatively eusocial sweat bee that exhibits multiple social phenotypes within one population and may therefore represent a transition between solitary and social reproduction. I use this …
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Dual-omics approach for 3,4-dihydroisocoumarin characterisation from Hydrangea serrata and isolation of polyketide synthases for heterologous expression in Pseudomonas putida KT2440
… and differential gene expression. A de-novo transcriptome assembly of leaves and roots alongside with functional annotation was generated and examined in two ways. The aim of this work was to isolate new polyketide synthase homologues from H. serrata with prospective of heterologous …
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Transcriptomic study of evolution and gene expression in diploid and allotetraploid glycine subgenus glycine
… wild relatives. We leveraged the use of de novo transcriptome assembly to gain access to the transcriptome of the perennial wild relatives of soybean. Using 2,430 orthologous genes shared between soybean and the perennial wild Glycine we perform test to detect signature of selection acting on the …
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Elucidation of the Function of Dihydrochalcones in Apple
… accumulating sieboldin. Moreover, a de novo transcriptome assembly was carried out in an intergeneric hybrid between M. x domestica and Pyrus communis L. known to accumulate intermediate levels of DHCs compared to apple, in order to identify additional genes potentially involved in DHC …
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Phenotypic and genetic variation in an Apios americana breeding collection; and characterization of the HD-Zip gene family, involved in abiotic stress responses in Glycine max
… yields - up to 1,515 g of tuber yield/plant. Transcriptome sequencing of multiple tissues from a single genotype generated both a high-quality de novo reference transcriptome assembly and an expression catalog. Re-sequencing of the leaf transcriptome from all the genotypes in the collection …
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Bayesian Modeling for Isoform Identification and Phenotype-specific Transcript Assembly
… identification and phenotype-specific transcript assembly. For isoform identification, we develop a computational approach, SparseIso, to jointly model the existence and abundance of isoforms in a Bayesian framework. A spike-and-slab prior is incorporated into the model to enforce the sparsity of …