GEO DataSets

(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) Background: Lactococcus garvieae is a bacterial pathogen that affects different animal species and human. Despite the widespread distribution and emerging clinical significance of L. garvieae in both veterinary and human medicine, there is almost a complete lack of knowledge about the genetic content of this microorganism. In the present study the genomic content of L. garvieae CECT 4531 was analyzed by bioinformatic tools and microarray-based comparative genomic hybridizations (CGH) experiments, using Lactococcus lactis subsp. more...

Organism:

Lactococcus lactis subsp. lactis; Lactococcus garvieae; Lactococcus lactis subsp. lactis Il1403; Streptococcus pneumoniae

Type:

Genome variation profiling by array

Platforms:

GPL5781 GPL9532

32 Samples

Download data: TXT

(Submitter supplied) We present a novel method of using commercial oligonucleotide expression microarrays for aCGH, enabling DNA copy number measurements and expression profiles to be combined using the same platform. This method yields aCGH data from genomic DNA without complexity reduction at a median resolution of approximately 17,500 base pairs. Due to the well-defined nature of oligonucleotide probes, DNA amplification and deletion can be defined at the level of individual genes and can easily be combined with gene expression data. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by array

Platform:

GPL570

8 Samples

Download data: CEL

(Submitter supplied) Background: Array comparative genomic hybridization (aCGH) is commonly used to screen different types of genetic variation in humans and model species. Here, we performed aCGH using an oligonucleotide gene-expression array for a non-model species, the intertidal snail Littorina saxatilis. First, we tested what types of genetic variation can be detected by this method using direct re-sequencing and comparison to the Littorina genome draft. more...

Organism:

Littorina saxatilis; Littorina fabalis; Littorina compressa; Littorina arcana

Type:

Genome variation profiling by array

Platform:

GPL19000

36 Samples

Download data: PAIR

(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; Prochlorococcus marinus str. MIT 9313; 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; 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

Type:

Other

Platform:

GPL6012

28 Samples

Download data: GPR

(Submitter supplied) LOCUS AM406671 2529478 bp DNA circular BCT 31-JAN-2007 DEFINITION Lactococcus lactis subsp. cremoris MG1363, complete genome. ACCESSION AM406671 VERSION AM406671.1 GI:124491690 KEYWORDS complete genome. SOURCE Lactococcus lactis subsp. cremoris MG1363 The complete genome sequence of the lactic acid bacterial paradigm Lactococcus lactis subsp. cremoris MG1363. more...

Organism:

Lactococcus cremoris subsp. cremoris MG1363

4 Series

17 Samples

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(Submitter supplied) BACKGROUND: Microarray comparative genomic hybridization (CGH) is currently one of the most powerful techniques to measure DNA copy number in large genomes. In humans, microarray CGH is widely used to assess copy number variants in healthy individuals and copy number aberrations associated with various diseases, syndromes and disease susceptibility. In model organisms such as Caenorhabditis elegans (C. more...

Organism:

Caenorhabditis elegans; Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platforms:

GPL7085 GPL7084

3 Samples

Download data: PAIR

(Submitter supplied) Genomic profiles of DLBCL (Diffuse Large B-cell Lymphoma) patients 20 DLBCL patients were selected for detection of genomic aberrations

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL9798

20 Samples

Download data: TXT

(Submitter supplied) Genomic profiles of CLL (Chronic Lymphocytic Leukemia) patients. 11 CLL patients were selected for detection of genomic aberrations, 8 patients with atypical CLL and 3 patients with typical CLL.

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL11069

11 Samples

Download data: TXT

(Submitter supplied) Profiling the genomic profiles of mental retardation patients. 13 mental retardation patients were selected for detection of genomic aberrations.

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL9796

13 Samples

Download data: TXT

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

Type:

Genome variation profiling by array

Platform:

GPL9990

12 Samples

Download data: TXT

(Submitter supplied) See manufacturer's website (www.affymetrix.com).

Organism:

Pseudomonas aeruginosa PAO1

1 Series

3 Samples

Download data: BPMAP, FASTA, GRC

(Submitter supplied) Pangenome arrays contain DNA oligomers targeting several sequenced reference genomes from the same species. In microbiology these can be employed to investigate the often high genetic variability within a species by comparative genome hybridization (CGH). The biological interpretation of pangenome CGH data depends on the ability to compare strains at a functional level, particularly by comparing the presence or absence of orthologous genes. more...

Organism:

Lactococcus lactis; Lactococcus cremoris; Lactococcus lactis subsp. lactis; Lactococcus lactis subsp. hordniae

Type:

Genome variation profiling by genome tiling array

Platform:

GPL7231

39 Samples

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(Submitter supplied) DNA methylation is often inversely correlated with gene expression. We used custom Nimblegen microarrays to determine the relationship between DNA methylation and gene expression in 6 iPS cell lines and the fibroblasts from which they were derived.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL9275

12 Samples

Download data: PAIR

(Submitter supplied) The use of a graduated series of Arabidopsis thaliana genomic deletion mutations (of sizes ranging from 4 bp to ~5 kb) to optimize CGH-based genomic deletion detection

Organism:

Arabidopsis thaliana

Type:

Genome variation profiling by genome tiling array

Platform:

GPL18327

5 Samples

Download data: PDF, TXT