Ontology highlight
ABSTRACT:
PROVIDER: PRJNA325617 | ENA |
REPOSITORIES: ENA
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Project description:Genotyping studies suggest that there is genetic variability among P. gingivalis strains, however the extent of variability remains unclear, and the regions of variability have only partially been identified. We previously used heteroduplex analysis of the ribosomal operon intergenic spacer region (ISR) to type P. gingivalis strains in several diverse populations, identifying 6 predominant heteroduplex types and many minor ones. In addition we used ISR sequence analysis to determine the relatedness of P. gingivalis strains to one another, and demonstrated a link between ISR sequence phylogeny and the disease-associated phenotype of P. gingivalis strains. The availability of whole genome microarrays based on the genomic sequence of strain W83 has allowed a more comprehensive analysis of P. gingivalis strain variability, using the entire genome. The objectives of this study were to define the phylogeny of P. gingivalis strains using the entire genome, to compare the phylogeny based on genome content to the phylogeny based on a single locus (ISR), and to identify genes that are associated with the strongly disease-associated strain W83 that could be important for virulence. Keywords: Comparative genomic hybridization
2008-10-09 | GSE13128 | GEO
Project description:Genotyping studies suggest that there is genetic variability among P. gingivalis strains, however the extent of variability remains unclear, and the regions of variability have only partially been identified. We previously used heteroduplex analysis of the ribosomal operon intergenic spacer region (ISR) to type P. gingivalis strains in several diverse populations, identifying 6 predominant heteroduplex types and many minor ones. In addition we used ISR sequence analysis to determine the relatedness of P. gingivalis strains to one another, and demonstrated a link between ISR sequence phylogeny and the disease-associated phenotype of P. gingivalis strains. The availability of whole genome microarrays based on the genomic sequence of strain W83 has allowed a more comprehensive analysis of P. gingivalis strain variability, using the entire genome. The objectives of this study were to define the phylogeny of P. gingivalis strains using the entire genome, to compare the phylogeny based on genome content to the phylogeny based on a single locus (ISR), and to identify genes that are associated with the strongly disease-associated strain W83 that could be important for virulence. Keywords: Comparative genomic hybridization Comparative genomic analysis of 7 clinically prevalent P. gingivalis strains was performed, using whole genome microarrays based on the sequence of strain W83. Strain W83 was the reference strains and there were 6 test strains. Flip-dye replicates were performed.
2010-05-18 | E-GEOD-13128 | biostudies-arrayexpress
Project description:Cancer is a disease of the genome. Many genomic abnormalities have been found in a variety of cancer types, which are believed to be attributable to tumorigenesis as well as resistance to treatment and recurrence. Genomic heterogeneity in the same type of cancer or within a tumor reveals the complexity of cancer biology so that intratumor heterogeneity has become an inherent feature of cancer. In this study, we use whole-exome sequencing and array comparative genomic hybridization technology to examine the mutational profiling and copy number changes from multi-region samples within an esophageal cancer in order to understand the genomic phylogeny in the evolution of intratumor heterogeneity in esophageal cancer.
2014-12-31 | GSE60625 | GEO
Project description:Analysis of DNA from 94 oral lesions by whole genome tiling-path array comparative genomic hybridization. Keywords: array comparative genomic hybridization
2008-12-31 | GSE9193 | GEO
Project description:Analysis of DNA from 89 oral lesions by whole genome tiling-path array comparative genomic hybridization. Keywords: array comparative genomic hybridization
2009-07-01 | GSE11275 | GEO
Project description:Over the last century, rainbow trout (RBT) has been widely used as a biological model in many biological disciplines and has become one of the best-studied fish. For example, RBT is an excellent model to study gene evolution as it is a partially tetraploid organism that underwent a whole-genome duplication (salmonid-specific 4th WGD) followed by a partial re-diploidization and significant genome rearrangements. In the meantime, RBT domestication spread quickly and globally to six continents for aquaculture and recreation. Efforts to sequence a pangenome reference have begun, and genome sequence is available for at least three rainbow trout clonal lines. However, epigenome reference annotations are needed to understand the functional genomic basis of RBT's phenotypic, environmental, and evolutional variations. This study provides a comprehensive catalog and epigenome annotation tracks of the rainbow trout. Gene regulatory elements, including chromatin histone modifications, chromatin accessibility, and DNA methylation, were identified by integrating data from ChIP-seq, ATAC-seq, and Methyl Mini-seq across RBT tissues together with RNA-seq gene expression data sets.
2024-10-03 | GSE245212 | GEO
Project description:Comparative genomic hybridization of strains PN1 (no duplication) and PN1400 (duplication in Chromosome 3)
2018-05-31 | GSE107099 | GEO
Project description:The availability of a reference genome assembly for Atlantic salmon, Salmo salar, SNP genotyping platforms and low cost sequencing is enhancing the understanding of both life history and production-related traits in this important commercial species. We collected and analysed transcriptomes from selected tissues of Atlantic salmon to inform future functional and comparative genomics studies. Messenger RNA (mRNA) was isolated from brain, pituitary, ovary and liver before Illumina sequencing produced a total of 640 million 150-bp paired-end reads. Following read mapping, feature counting and normalization, cluster analysis identified genes highly expressed in a tissue-specific manner. Functional profiling identified gene clusters describing the unique functions of each tissue. Moreover, highly-expressed transcription factors present in each tissue-specific gene cluster were identified. The data and analysis presented are relevant to the emerging Functional Annotation of All Salmonid Genomes (FAASG) initiative that is seeking to develop a detailed understanding of both salmonid evolution and the genomic elements that drive gene expression and regulation.
2018-08-22 | GSE114247 | GEO