GEO DataSets

(Submitter supplied) comparative genomic hybridization between Burkholderia cepacia sequenced strains to determine what are the limits to strain relativity in order to still provide accurate estimations of gene content

Organism:

Burkholderia cenocepacia; Burkholderia vietnamiensis G4; Burkholderia cenocepacia HI2424; Burkholderia orbicola; Burkholderia cenocepacia J2315; Paraburkholderia xenovorans LB400; Burkholderia ambifaria AMMD

Type:

Genome variation profiling by array

Platform:

GPL9990

12 Samples

Download data: TXT

(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) The publicly available genome sequence information of two rice strains, japonica cultivar Nipponbare and indica cultivar 93-11, opens a great opportunity for investigation of performances DNA genotyping by high-density oligonucleotide arrays. Here, we compare single feature polymorphism (SFP) detection performances between whole genome hybridization and transcript hybridization using Affymetrix Rice Expression Array and the two rice cultivars.

Organism:

Oryza sativa; Oryza sativa Indica Group; Oryza sativa Japonica Group

Type:

Expression profiling by array; Genome variation profiling by array

Platform:

GPL2025

27 Samples

Download data: CEL, CHP

(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:

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 crenarchaeote 74A4; uncultured proteobacterium 65D09; uncultured marine group II euryarchaeote EF100_57A08; uncultured marine bacterium EB000_55B11; Prochlorococcus marinus str. MIT 9313; uncultured proteobacterium; Prochlorococcus marinus str. MIT 9515; uncultured marine bacterium 577; uncultured gamma proteobacterium eBACHOT4E07; 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) See Talla et al. 2003 (PMID : 14499002)

Organism:

Saccharomyces cerevisiae

1 Series

22 Samples

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(Submitter supplied) See Talla et al. 2003 (PMID : 14499002)

Organism:

Saccharomyces cerevisiae

1 Series

18 Samples

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(Submitter supplied) The yeast 5803 ORFs MicroArray is composed of 32 subgrids, which follow a pattern of 8 metarows and 4 metacolumns. Each subgrid contains 20 columns and 20 rows with a dot spacing of 200 µm. Probes are spotted as closed duplicates. In order to provide a friendly environment, the first subgrid row on each array metarow contains all the normalization controls, which include the controls with serial dilution of the Renilla LuxA cDNA PCR product. more...

Organism:

Saccharomyces cerevisiae

3 Series

16 Samples

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(Submitter supplied) The yeast 5803 ORFs MicroArray is composed of 32 subgrids, which follow a pattern of 8 metarows and 4 metacolumns. Each subgrid contains 20 columns and 20 rows with a dot spacing of 200 µm. Probes are spotted as closed duplicates. In order to provide a friendly environment, the first subgrid row on each array metarow contains all the normalization controls, which include the controls with serial dilution of the Renilla LuxA cDNA PCR product. more...

Organism:

Saccharomyces cerevisiae

1 Series

6 Samples

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(Submitter supplied) Background Array-based comparative genome hybridization (aCGH) is commonly used to determine the genomic content of bacterial strains. In aCGH data, systematic errors are comparable to those occurring in transcriptome data. However, especially for microbes, an additional source of variation exists: differences in hybridization due to gene sequence divergence between the strains hybridized. Current normalization methods do not take this source of variation into consideration. more...

Organism:

Lactococcus lactis subsp. lactis Il1403; Lactococcus cremoris subsp. cremoris MG1363

Type:

Genome variation profiling by array

Platform:

GPL2545

4 Samples

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(Submitter supplied) The new microarray described for Mycobacterium tuberculosis in our study has a more complete reprensentation of the genome than any other array design reported till date. Further, protocols for sample preparation, labelling and hybridisation for accurate gene expression profiling of M.tuberculosis have been optimised.

Organism:

Mycobacterium tuberculosis H37Rv

Type:

Expression profiling by array

Platform:

GPL16972

28 Samples

Download data: TXT

(Submitter supplied) Background Bordetella pertussis is a Gram-negative bacterium that infects the human respiratory tract and causes pertussis or whooping cough. The disease has resurged in many countries including Finland where the whole-cell pertussis vaccine has been used for more than 50 years. Antigenic divergence has been observed between vaccine strains and clinical isolates in Finland. To better understand genome evolution in B. more...

Organism:

Bordetella pertussis

Type:

Genome variation profiling by array

Platform:

GPL5378

26 Samples

Download data: TXT

(Submitter supplied) We have developed a 60-mer oligonucleotide multibacterial microarray for detection and expression profiling of biodegradative genes and bacterial diversity (16S rRNA gene) in different habitats contaminated with varieties of hazardous chemicals. The genes selected were involved in biodegradation and biotransformation of various groups of compounds viz. nitroaromatic compounds (148 genes), chloroaromatic compounds (75 genes), monoaromatic compounds (373 genes), polyaromatic hydrocarbons (174 genes), pesticides/ herbicides (34 genes), alkanes/aliphatics (185 genes) and heavy metals (68 genes), which covered a total number of 133 chemicals. more...

Organism:

Escherichia coli BL21; freshwater sediment metagenome; synthetic construct; Escherichia coli DH5[alpha]; Escherichia coli K-12; Sphingomonas sp. NM05; soil metagenome; Rhodococcus jostii RHA1; Bordetella sp. IITR-02

Type:

Genome variation profiling by array

Platform:

GPL10926

17 Samples

Download data: TXT

(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:

Micrococcus luteus; 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

Type:

Genome variation profiling by array

Platform:

GPL8295

23 Samples

Download data: PAIR