Ontology highlight
ABSTRACT:
PROVIDER: PRJEB35015 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Creation of a new library entries for Candida auris using MALDI Biotyper. Candida auris has a high genetic variability in the world, the identification of Colombian isolates is difficult using the main Bruker library. A new in-house library was created using Colombian isolated and was validated using 300 isolated strains
2020-06-02 | PXD016387 | Pride
Project description:Chikungunya virus (CHIKV) infection is characterized by alterations in gene expression profile on host cells that consequently lead to an immune response. Here, we used RNA sequencing to analyze the mRNA expression profile in human monocyte-derived macrophages (MDMs) infected with a Colombian clinical isolate of CHIKV at 6 and 24 hpi. analyze the mRNA expression profile in the human monocyte-derived macrophages infected at 6 and 24 hrs with a Colombian clinical isolate of Chikungunya virus.
2022-01-19 | GSE193977 | GEO
Project description:Microarrays have become a powerful tool for DNA-based molecular diagnostics and identification of pathogens. However, most of them target a limited range of organisms and are generally based on only one or very few genes for organism identification. Although such microarrays are proven tools for species identification, they suffer from the fact that identification is only possible for organisms for which probes were specifically pre-developed. Furthermore, this approach often leads to problems with taxonomic-level resolution with insufficient diagnostic differences between closely related taxa found in the commonly used DNA sequences. An alternative strategy is to use the hybridisation pattern generated by many different anonymous markers distributed over the entire genome for identification based on comparison to a type database. We realised this strategy using a high density microarray containing 95,000 different 13-mer probes. Here, we demonstrate the specificity of our microarray based on results obtained with nine different bacterial species and strains. The hybridisation patterns allowed clear differentiation at the strain and even variant level. The reproducibility of our system was high as shown by high correlation coefficients between replicates, despite the occurrence of mismatch hybridisation. The results indicate the potential for identification of all bacterial taxa at the subspecies level using our universal microarray.
2010-03-16 | GSE15391 | GEO
Project description:Microarrays have become a powerful tool for DNA-based molecular diagnostics and identification of pathogens. However, most of them target a limited range of organisms and are generally based on only one or very few genes for organism identification. Although such microarrays are proven tools for species identification, they suffer from the fact that identification is only possible for organisms for which probes were specifically pre-developed. Furthermore, this approach often leads to problems with taxonomic-level resolution with insufficient diagnostic differences between closely related taxa found in the commonly used DNA sequences. An alternative strategy is to use the hybridisation pattern generated by many different anonymous markers distributed over the entire genome for identification based on comparison to a type database. We realised this strategy using a high density microarray containing 95,000 different 13-mer probes. Here, we demonstrate the specificity of our microarray based on results obtained with nine different bacterial species and strains. The hybridisation patterns allowed clear differentiation at the strain and even variant level. The reproducibility of our system was high as shown by high correlation coefficients between replicates, despite the occurrence of mismatch hybridisation. The results indicate the potential for identification of all bacterial taxa at the subspecies level using our universal microarray. Hybridisation patterns of DNA from bacterial type strains (E. coli strains K12 and B, Pantoea agglomerans strains ATCC27155T and C9-1, Pantoea stewartii pv stewartii strain DC283, Salmonella Typhimurium strains LT2 and DT204 and Micrococcus luteus) were compared to each other. Using GeneSpring v7.3.1, cluster analyses were performed as well as ANOVA in order to determine the more discriminative probes out of our 95,000-probe panel.
2010-05-06 | E-GEOD-15391 | biostudies-arrayexpress
Project description:Flash proteotyping is a methodology for ultra-fast identification of microorganisns by tandem mass spectrometry. Here, we obtained results on five reference strains and ten new bacterial isolates. The methodology is based on direct sample infusion into the mass spectromete and an original, highly sensitive procedure for data processing and taxonomic identification.
2023-12-21 | PXD045510 | Pride
Project description:Potato yellow vein virus (PYVV) was detected by RT-PCR in potatoes grown in the Central Colombian highlands, north of Bogotá (~3000 mt height). At this altitude viral whitefly vectors are largely absent, but infection persists because of the use of uncertified tubers. Plants with typical PYVV-induced yellowing symptoms, as well as with atypical yellowing or non-symptomatic were sampled at three separate geographical locations. And five of them were subjected to Next Generation Sequencing (NGS) of their small RNA (sRNA) populations. Contigs to any virus were assembled, and complete or almost complete sequences of four PYVV isolates were thus re-constructed, all from symptomatic plants. Three viral isolates infected plants singly, while the fourth one co-infected the plant together with a potyvirus (potato virus Y, PVY). Relative proportions of sRNAs to each of the three viral genomic RNAs were assessed and found to remain comparable between the four infections. Genomic regions were identified as hotspots to sRNA formation, or as regions that induced poorly sRNAs. Furthermore, PYVV titers in the mixed vs. the single infections were found to be remained comparable, indicating absence of synergistic/antagonistic effect of the potyvirus on the accumulation of PYVV.
2021-03-03 | GSE157752 | GEO
Project description:Genome sequencing of native Colombian strains of Clostridium sp.
| PRJNA255517 | ENA
Project description:Taxonomic study of Antarctic environmental strains
| PRJNA791544 | ENA