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VLA lyssavirus genotyping dataset

ABSTRACT: Data from the VLA lyssavirus genotyping microarray. The array platform for this data is GEO accession GPL8066, and consists of 624 oligos representing two viral families. The data set itself consists of 14 arrays, 7 hybridised with RNA from mice brains infected with 7 genotypes of lyssaviruses, 1 hybridised with RNA from normal mouse brain, and 6 hybridised with RNA from coded samples consisting of infected mouse brains or control mouse brains. Keywords: Lyssavirus genotyping microarray

ORGANISM(S): Lyssavirus lagos Lyssavirus rabies Lyssavirus australis European bat lyssavirus 1 European bat lyssavirus 2 Lyssavirus duvenhage Viruses Lyssavirus mokola unidentified

PROVIDER: GSE14705 | GEO | 2009/06/09

SECONDARY ACCESSION(S): PRJNA112087

REPOSITORIES: GEO

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VLA lyssavirus genotyping dataset

Project description:Data from the VLA lyssavirus genotyping microarray. The array platform for this data is GEO accession GPL8066, and consists of 624 oligos representing two viral families. The data set itself consists of 14 arrays, 7 hybridised with RNA from mice brains infected with 7 genotypes of lyssaviruses, 1 hybridised with RNA from normal mouse brain, and 6 hybridised with RNA from coded samples consisting of infected mouse brains or control mouse brains. Keywords: Lyssavirus genotyping microarray Data from the VLA lyssavirus genotyping microarray. The array platform for this data is GEO accession GPL8066, and consists of 624 oligos representing two viral families. The data set itself consists of 14 arrays, 7 hybridised with RNA from mice brains infected with 7 genotypes of lyssaviruses, 1 hybridised with RNA from normal mouse brain, and 6 hybridised with RNA from coded samples consisting of infected mouse brains or control mouse brains. Statistical analysis of the data was done with DetectiV software (Watson et al., 2007). The median and array methods of normalization were used in the statistical analysis of the results. In the median method, DetectiV software calculates the mean fluorescence for each set of probes and normalised against background fluorescence of all probes, assuming that most probes are not hybridized. The array method utilizes an entire control array, e.g. RNA from a known uninfected animal, as the negative control and all probe values are divided by their respective elements from the control array.

2010-05-18 | E-GEOD-14705 | biostudies-arrayexpress

IAH/VLA VA1 Virus Detection Array Dataset

Project description:Data from the IAH/VLA diagnostic pathogen/virus detection microarray. The array platform for this data is GEO accession GPL5725 (provisional), and consists of 5824 oligos representing over 100 viral families, species and subtypes. The data set itself consists of 12 arrays, 4 hybridised with RNA from cell cultured foot-and-mouth disease virus (FMDV) type O, 3 hybridised with RNA from FMDV type A, 1 hybridised with RNA from a sheep infected with FMDV type O, and 4 hybridised with cell-cultured Avian Infectious Bronchitis virus (IBV). Keywords: Virus Detection Microarray

2007-08-14 | GSE8746 | GEO

VLA lyssavirus genotyping dataset

Project description:VLA lyssavirus genotyping dataset

| PRJNA112087 | ENA

Genotyping SAX1 Mouse Human Hybrid

Project description:Genotyping SAX1 Mouse Human Hybrid to identify haplotypes of chromosomes 7 and X

2010-08-27 | GSE23816 | GEO

Optimal Processing for Proteomic Genotyping of Single Human Hairs

Project description:The human hair proteome offers new insight in the field of human identification. Hair often contains DNA that has been degraded due to the process of cornification. The smaller fragments of DNA present a challenge for obtaining useful information concerning the identity of the donor. Proteomic genotyping offers an alternative approach which starts with protein, a biomolecule abundant in the hair shaft. Nonsynonymous single nucleotide polymorphisms may be detected in the sequence of these proteins, allowing the inference of SNP genotypes. Population genetics-based information from these genotypes may be used to calculate random match probability or even infer ancestry. The current challenge of this research is to optimize processing chemistry in order to maximize genetic information from a single human hair shaft. Results indicate that optimal conditions for proteomic analysis of a single human hair include 6 hrs of reduction with 100 mM dithiothreitol at room temperature, alkylation with 200 mM iodoacetamide for 45 min, and 6 hrs of digestion with two 1:50 (enzyme:protein) additions of stabilized trypsin at room temperature, with stirring incorporated into all three steps. Our final conditions using optimized temperatures and incubation times for disulfide reduction and protein digestion produced random match probabilities of up to 1 in 624 million from a single hair with a median value of 1 in 1.1 million, compared to a maximum random match probability of 1 in 1380 and a median value of 1 in 24 for the original processing method.

2020-06-10 | PXD016155 | Pride

Genotyping SAX1 Mouse Human Hybrid

Project description:Genotyping SAX1 Mouse Human Hybrid

| PRJNA133157 | ENA

Genotyping in Neuroblastoma Primary tumors

Project description:We performed genotyping of Neuroblastoma Primary tumors using Illumina HumanHap 550 - v1,v3,v3duo and 610 Quad genotyping beadchips.

2011-09-15 | GSE19385 | GEO

Genotyping human lymphoblastoid cell lines

Project description:Genotyping FATO and SATO3 human lymphoblastoid cell lines

2010-08-27 | GSE23813 | GEO

NABEC NeuroChip Genotyping

Project description:NABEC NeuroChip Genotyping

| PRJNA408203 | ENA

Genotyping of Coxiella burnetii strains collection

Project description:Genotyping based on genomic comparative hybridization of different isolates of coxiella burnetii compared to NMI reference strain

2011-12-31 | GSE31543 | GEO

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