Viral Microarray - Control Set
Ontology highlight
ABSTRACT:
OTHER RELATED OMICS DATASETS IN: GSE21319
PROVIDER: PRJNA129467 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Viral Microarray - Cultured Virus Set
| PRJNA129469 | ENA
Project description:Background: The analysis of oligonucleotide microarray data in pathogen surveillance and discovery assays is a challenging task. Target template concentration, nucleic acid integrity, and host nucleic acid composition can each have a profound effect on signal distribution. Exploratory analysis of fluorescent signal distribution in clinical samples has revealed deviations from normality, suggesting that distribution-free approaches should be applied. Results: An examination of both positive predictive value and false positive rates was employed to assess the utility of three well-established nonparametric methods for the analysis of viral array hybridization data: (1) Mann-Whitney U, (2) the Spearman correlation coefficient and (3) the chi-square test. Of the three tests, it was the chi-square that proved most useful. Conclusions: The acceptance of microarray use for routine clinical diagnostics will require that the technology be accompanied by simple yet reliable analytic methods. We report that our implementation of the chi-square test yielded a combination of low false positive rates and a high degree of predictive accuracy. A set of comprehensive probes covering vertebrate viruses was designed and printed using Agilent in-situ fabrication. Cells in tissue culture were infected with West Nile Virus, then RNA was harvested. RNA was converted to cDNA, then copy number was quantified by quantatative real-time PCR. RNA stocks were diluted to 10^4 or 10^6 copies per microliter then converted to cDNA, amplified, labeled and hybridized to the array. Human Lung RNA was used as a control and spiked in at 10ng or 200ng.
2010-05-24 | E-GEOD-21317 | biostudies-arrayexpress
Project description:Background: The analysis of oligonucleotide microarray data in pathogen surveillance and discovery assays is a challenging task. Target template concentration, nucleic acid integrity, and host nucleic acid composition can each have a profound effect on signal distribution. Exploratory analysis of fluorescent signal distribution in clinical samples has revealed deviations from normality, suggesting that distribution-free approaches should be applied. Results: An examination of both positive predictive value and false positive rates was employed to assess the utility of three well-established nonparametric methods for the analysis of viral array hybridization data: (1) Mann-Whitney U, (2) the Spearman correlation coefficient and (3) the chi-square test. Of the three tests, it was the chi-square that proved most useful. Conclusions: The acceptance of microarray use for routine clinical diagnostics will require that the technology be accompanied by simple yet reliable analytic methods. We report that our implementation of the chi-square test yielded a combination of low false positive rates and a high degree of predictive accuracy.
2010-05-24 | GSE21317 | GEO
Project description:Background: The analysis of oligonucleotide microarray data in pathogen surveillance and discovery assays is a challenging task. Target template concentration, nucleic acid integrity, and host nucleic acid composition can each have a profound effect on signal distribution. Exploratory analysis of fluorescent signal distribution in clinical samples has revealed deviations from normality, suggesting that distribution-free approaches should be applied. Results: An examination of both positive predictive value and false positive rates was employed to assess the utility of three well-established nonparametric methods for the analysis of viral array hybridization data: (1) Mann-Whitney U, (2) the Spearman correlation coefficient and (3) the chi-square test. Of the three tests, it was the chi-square that proved most useful. Conclusions: The acceptance of microarray use for routine clinical diagnostics will require that the technology be accompanied by simple yet reliable analytic methods. We report that our implementation of the chi-square test yielded a combination of low false positive rates and a high degree of predictive accuracy. A set of comprehensive probes covering vertebrate viruses was designed and printed using Agilent in-situ fabrication. Cells in tissue culture were infected with various viruses, then RNA was harvested. RNA was converted to cDNA, then amplified, labeled and hybridized to the array.
2010-05-24 | E-GEOD-21318 | biostudies-arrayexpress
Project description:Background: The analysis of oligonucleotide microarray data in pathogen surveillance and discovery assays is a challenging task. Target template concentration, nucleic acid integrity, and host nucleic acid composition can each have a profound effect on signal distribution. Exploratory analysis of fluorescent signal distribution in clinical samples has revealed deviations from normality, suggesting that distribution-free approaches should be applied. Results: An examination of both positive predictive value and false positive rates was employed to assess the utility of three well-established nonparametric methods for the analysis of viral array hybridization data: (1) Mann-Whitney U, (2) the Spearman correlation coefficient and (3) the chi-square test. Of the three tests, it was the chi-square that proved most useful. Conclusions: The acceptance of microarray use for routine clinical diagnostics will require that the technology be accompanied by simple yet reliable analytic methods. We report that our implementation of the chi-square test yielded a combination of low false positive rates and a high degree of predictive accuracy.
2010-05-24 | GSE21318 | GEO
Project description:MicroArray Quality Control (MAQC) Project
| PRJNA96213 | ENA
Project description:MicroArray Quality Control Phase II (MAQC-II) Project
| PRJNA117475 | ENA
Project description:Ependymoma subpopulation lineages underlie clinical classification and outcome (microarray data set)
| PRJNA517721 | ENA
Project description:CD8+ T cell responses to chronic infection are sustained by stem-like cells, which differentiate into effector-like cells mediating some level of pathogen control; however persistent antigen progressively impairs their effector functions. Understanding the molecular control of stem-like cell differentiation to improve durability of functional T cell responses has important therapeutic implications. Here, we found that the chemokine receptor CXCR3 was highly expressed on viral-specific stem-like CD8+ T cells and that one of its ligands, CXCL10, regulated the persistence and heterogeneity of responding CD8+ T cells in spleens of mice chronically infected with lymphocytic choriomeningitis virus. CXCL10 was produced by inflammatory monocytes and fibroblasts of the splenic red pulp where it granted stem-like cells access to signals promoting differentiation and limited their exposure to pro-survival niches in the white pulp. Consequently, the magnitude of functional CD8+ T cell responses was greater in Cxcl10-/- mice and was associated with a lower viral set point.
2021-10-13 | GSE185746 | GEO
Project description:Drosophila melanogaster Set, Set, is expressed in 3 baseline experiment(s);
| FBgn0014879 | ExpressionAtlas