GEO DataSets

(Submitter supplied) Emerging known and unknown pathogens create profound threats to public health. Platforms for rapid detection and characterization of microbial agents are critically needed to prevent and respond to disease outbreaks. Available detection technologies cannot provide broad functional information about known and novel organisms. As a step toward developing such a system, we have produced and tested a series of high-density functional gene arrays to detect elements of virulence and antibiotic resistance mechanisms. more...

Organism:

Staphylococcus aureus; Escherichia coli O157:H7 str. EDL933; Enterococcus faecalis V583; Salmonella enterica; unidentified; Staphylococcus aureus subsp. aureus Mu50; Escherichia coli CFT073; Streptococcus pyogenes MGAS5005; Staphylococcus saprophyticus; Escherichia coli str. K-12 substr. MG1655

Type:

Other

Platform:

GPL6656

12 Samples

Download data: PAIR

(Submitter supplied) 60-mers oligonucleotide probes, in-situ synthesis on 1 Protocol: Sure Print Technology-In situ synthesis

Organism:

Staphylococcus aureus

4 Series

30 Samples

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(Submitter supplied) Microarrays are useful tools for detecting and quantifying specific functional and phylogenetic genes in natural microbial communities. In order to track uncultivated microbial genotypes and their close relatives in an environmental context, we designed and implemented a “genome proxy” microarray that targets microbial genome fragments recovered directly from the environment. Fragments consisted of sequenced clones from large-insert genomic libraries from microbial communities in Monterey Bay, the Hawaii Ocean Time-series station ALOHA, and Antarctic coastal waters. more...

Organism:

Prochlorococcus marinus str. MIT 9313; Prochlorococcus marinus str. MIT 9515; uncultured marine bacterium 577; uncultured gamma proteobacterium eBACHOT4E07; uncultured crenarchaeote 4B7; Prochlorococcus marinus subsp. pastoris str. CCMP1986; Prochlorococcus marinus str. MIT 9312; uncultured marine gamma proteobacterium EBAC31A08; uncultured marine bacterium EB0_41B09; uncultured proteobacterium 60D04; uncultured marine alpha proteobacterium; uncultured Pseudomonadota bacterium; uncultured crenarchaeote 74A4; uncultured proteobacterium 65D09; uncultured marine group II euryarchaeote EF100_57A08; uncultured marine bacterium EB000_55B11; uncultured marine group II euryarchaeote 37F11; uncultured marine bacterium 440; uncultured marine bacterium 583; marine metagenome

Type:

Other

Platform:

GPL6012

28 Samples

Download data: GPR

(Submitter supplied) 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. more...

Organism:

Pantoea agglomerans; Escherichia coli B; synthetic construct; Pantoea stewartii; Salmonella enterica subsp. enterica serovar Typhimurium; Salmonella enterica subsp. enterica serovar Typhimurium str. LT2; Escherichia coli K-12; Micrococcus luteus

Type:

Genome variation profiling by array

Platform:

GPL8295

23 Samples

Download data: PAIR

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Bovine viral diarrhea virus 1; Human adenovirus 7; Human respiratory syncytial virus A strain Long; synthetic construct; Bluetongue virus 2; Human betaherpesvirus 6B; Human respiratory syncytial virus B1; Chlorocebus aethiops; Homo sapiens; Vaccinia virus Lister

Type:

Other

Platforms:

GPL11040 GPL11053

26 Samples

Download data: PAIR

(Submitter supplied) We designed a pan-Microbial Detection Array (MDA) to detect all known viruses (including phage), bacteria, and plasmids. Family-specific probes were selected for all sequenced viral and bacterial complete genomes, segments, and plasmids. Probes were designed to tolerate some sequence variation to enable detection of divergent species with homology to sequenced organisms. The array has wider coverage of bacterial and viral targets based on more recent sequence data and more probes per target than other microbial detection/discovery arrays in the literature. more...

Organism:

Homo sapiens; Vaccinia virus Lister; Human adenovirus 7; Human respiratory syncytial virus B1; Human respiratory syncytial virus A strain Long; Human betaherpesvirus 6B; synthetic construct; Bluetongue virus 2; Bovine viral diarrhea virus 1

Type:

Other

Platform:

GPL11053

7 Samples

Download data: PAIR

(Submitter supplied) We designed a pan-Microbial Detection Array (MDA) to detect all known viruses (including phage), bacteria, and plasmids. Family-specific probes were selected for all sequenced viral and bacterial complete genomes, segments, and plasmids. Probes were designed to tolerate some sequence variation to enable detection of divergent species with homology to sequenced organisms. The array has wider coverage of bacterial and viral targets based on more recent sequence data and more probes per target than other microbial detection/discovery arrays in the literature. more...

Organism:

Human betaherpesvirus 6B; Chlorocebus aethiops; Homo sapiens; Vaccinia virus Lister; Bovine viral diarrhea virus 1; synthetic construct

Type:

Other

Platform:

GPL11040

19 Samples

Download data: PAIR

(Submitter supplied) Approximatively 75% of the genome of S. aureus (“core” genome) are highly conserved between strains, whereas the remaining 25% (“accessory” genome) are composed of variable regions that are mostly composed of mobile genetic elements (MGE), containing virulence and resistance genes. We have developed a composite DNA-microarray (StaphVar Array) which selectively targets 403 genes located on the accessory or core variable genome. more...

Organism:

Staphylococcus aureus

Type:

Genome variation profiling by array

Platform:

GPL7684

26 Samples

Download data: GPR