GEO DataSets

(Submitter supplied) Submicroscopic (< 2 Mb) segmental DNA copy number changes are a recently recognized source of genetic variability between individuals. The biological consequences of copy number variants (CNVs) are largely undefined. CNVs have been detected in diverse species, including mice and humans. Published studies in mice have been limited by resolution and strain selection. We chose to study twenty-one well-characterized inbred mouse strains that are the focus of an international effort to measure, catalog, and disseminate phenotype data. more...

Organism:

Mus musculus

Type:

Genome variation profiling by genome tiling array

Platform:

GPL4276

31 Samples

Download data

(Submitter supplied) We have conducted a genome-wide analysis of spontaneous copy number variation (CNV) in the laboratory mouse. We used high resolution microarrays to identify 38 CNVs between 14 colonies of the C57BL/6 strain spanning ~967 generations of inbreeding, and examined these loci in 12 additional strains. It is clear from our results that many CNVs arise through a highly non-random process: 18 of 38 were the product of recurrent mutation, and rates of change vary roughly four orders of magnitude across different loci. more...

Organism:

Mus musculus

Type:

Genome variation profiling by genome tiling array

Platform:

GPL5824

336 Samples

Download data: GPR

(Submitter supplied) We have conducted a genome-wide analysis of spontaneous copy number variation (CNV) in the laboratory mouse. We used high resolution microarrays to identify 38 CNVs between 14 colonies of the C57BL/6 strain spanning ~967 generations of inbreeding, and examined these loci in 12 additional strains. It is clear from our results that many CNVs arise through a highly non-random process: 18 of 38 were the product of recurrent mutation, and rates of change vary roughly four orders of magnitude across different loci. more...

Organism:

Mus musculus

Type:

Genome variation profiling by genome tiling array

Platform:

GPL5777

68 Samples

Download data: FTR, PAIR

(Submitter supplied) The purpose of this experiment was to determine the expression traits in animals from F2 intercross of inbred strains C57BL/6J, C3H/HeJ. (N=309, 164 males and 145 females).

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL2510

292 Samples

Download data

(Submitter supplied) The purpose of this experiment was to determine the expression traits in animals from F2 intercross of inbred strains C57BL/6J, C3H/HeJ. (N=309, 164 males and 145 females).

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL2510

285 Samples

Download data

(Submitter supplied) The purpose of this experiment was to determine the expression traits in animals from F2 intercross of inbred strains C57BL/6J, C3H/HeJ. (N=309, 164 males and 145 females).

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL2510

302 Samples

Download data

(Submitter supplied) The purpose of this experiment was to determine the expression traits in animals from F2 intercross of inbred strains C57BL/6J, C3H/HeJ. (N=309, 164 males and 145 females).

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL2510

295 Samples

Download data: TXT

(Submitter supplied) HighRes-CGH arrays that utilize ≈385,000 distinct oligonucleotide probes to cover chromosome 22 at 85 bp resolution (tiling path step size) were designed and synthesized as previously described (Urban et al., Proc Natl Acad Sci U S A. 2006;103(12):4534-9; see also GSE4240 record). Here, two healthy individuals were studied using the same experimental protocols as in Urban et al. Keywords: high-resolution comparative genome hybridization using oligonucleotides

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL3448

2 Samples

Download data: TXT

(Submitter supplied) Following previous work, we extend the use of a reliable detection method to a wide progeny in white spruce in order to genetically map a maximum of inherited gene CNVs and linked those to phenotypic traits related to adaptation. We selected probes targeting 3911 genes likely in CNV in this progeny and performed genetic mapping for those harboring a 1:1 segregation. In addition, the link between gene CNVs and phenotypic variation was tested using budburst, budset and growth data for the same samples. more...

Organism:

Picea glauca

Type:

Genome variation profiling by array

Platform:

GPL23818

115 Samples

Download data: TXT

(Submitter supplied) Background The goat (Capra hircus) represents one of the most important farm animal species. It is reared in all continents with an estimated world population of about 800 million of animals. Despite its importance, studies on the goat genome are still in their infancy compared to those in other farm animal species. Comparative mapping between cattle and goat showed only a few rearrangements in agreement with the similarity of chromosome banding. more...

Organism:

Bos taurus; Capra hircus

Type:

Genome variation profiling by genome tiling array

Platform:

GPL10990

9 Samples

Download data: PAIR

(Submitter supplied) Copy number variations (CNVs) affect a wide range of phenotypic traits; however, CNVs in or near segmental duplication regions are often intractable. Using a read depth approach based on next-generation sequencing, we examined genome-wide copy number differences among five taurine (three Angus, one Holstein and one Hereford) and one indicine (Nelore) cattle. Within mapped chromosomal sequence, we identified 1,265 CNV regions comprising ~55.6 Mbp sequence-476 of which (~38%) have not previously been reported. more...

Organism:

Bos taurus

Type:

Genome variation profiling by genome tiling array

Platform:

GPL11314

5 Samples

Download data: PAIR, TXT

(Submitter supplied) Genomic structural variation is an important and abundant source of genetic and phenotypic variation. Here we describe the first systematic and genome-wide analysis of copy number variations (CNVs) in modern domesticated cattle using array comparative genomic hybridization (array CGH), quantitative PCR (qPCR) and fluorescent in situ hybridization (FISH). The array CGH panel included 90 animals from 11 Bos taurus, 3 Bos indicus and 3 composite breeds for beef, dairy or dual purpose. more...

Organism:

Bos taurus

Type:

Genome variation profiling by genome tiling array

Platforms:

GPL9865 GPL9866

90 Samples

Download data: PAIR, TXT

(Submitter supplied) This study centered on using a custom made Nimblegen aCGH chip that targeted all segmental duplications in the canine genome to identify associated CNVs. A total of 19 hybridizations were performed in a panel of diverse dogs and a single wolf.

Organism:

Canis lupus; Canis lupus familiaris

Type:

Genome variation profiling by genome tiling array

Platform:

GPL7501

19 Samples

Download data: PAIR, TXT

(Submitter supplied) Copy number variants (CNVs) reshape gene structure, modulate gene expression, and contribute to significant phenotypic variation. Previous studies have revealed CNV patterns in natural populations of Drosophila melanogaster and suggested that selection and mutational bias shape genomic patterns of CNV. While previous CNV studies focused on heterogeneous strains, here we established a number of second-chromosome substitution lines to uncover CNV characteristics when homozygous. more...

Organism:

Drosophila melanogaster

Type:

Genome variation profiling by array

Platform:

GPL6056

36 Samples

Download data: GPR

(Submitter supplied) Chromosomal structural variation can cause alterations in gene dosage and gene regulation between genomes. Structural variants producing a change in the number of copies of a genomic region are termed copy number variants (CNVs). CNVs have been demonstrated to have causative effects on both Mendelian and complex traits, including susceptibility to infectious diseases. We are interested in mapping CNVs to domesticated chicken breeds to help determine structural variation between genomes that influences economically important traits. more...

Organism:

Gallus gallus

Type:

Genome variation profiling by genome tiling array

Platform:

GPL11041

24 Samples

Download data: TXT

(Submitter supplied) Since CNVs play a vital role in genomic studies, it is an imperative need to develop a comprehensive, more accurate and higher resolution porcine CNV map with practical significance in follow-up CNV functional analyses To detect CNV of pigs, we performed high density aCGH data of diverse pig breeds in the framework of the pig draft genome sequence (Sscrofa10.2)

Organism:

Sus scrofa

Type:

Genome variation profiling by genome tiling array

Platform:

GPL17469

12 Samples

Download data: TXT

(Submitter supplied) Copy number variations (CNVs), which represent a significant source of genetic diversity in mammals, are currently being associated with phenotypes of clinical relevance, mostly in humans and mice. Notwithstanding, little is known about the extent of CNV that contributes to genetic variation in cattle. This study reports the highest resolution map of copy number variation in the cattle genome, with 304 CNV regions (CNVRs) being identified among the genomes of 20 bovine samples from 4 dairy and beef breeds. more...

Organism:

Bos taurus

Type:

Genome variation profiling by genome tiling array

Platforms:

GPL9220 GPL9221 GPL9219

114 Samples

Download data: PAIR

(Submitter supplied) The contribution to genetic diversity of genomic segmental copy number variations (CNVs) is less well understood than that of single-nucleotide polymorphisms (SNPs). While less frequent than SNPs, CNVs have greater potential to affect phenotype. In this study, we have performed the most comprehensive survey to date of CNVs in mice, analyzing the genomes of 42 Mouse Phenome Consortium priority strains. more...

Organism:

Mus musculus

Type:

Genome variation profiling by genome tiling array

Platform:

GPL4092

84 Samples

Download data: TXT

(Submitter supplied) Copy number variants (CNVs) are heritable gains and losses of genomic DNA in normal individuals. While copy number variation is widely studied in humans, our knowledge of CNVs in other mammalian species is more limited. We have designed a custom array-based comparative genomic hybridization (aCGH) platform with 385,000 oligonucleotide probes based on the reference genome sequence of the rhesus macaque (Macaca mulatta), the most widely studied non-human primate in biomedical research. more...

Organism:

Macaca mulatta

Type:

Genome variation profiling by genome tiling array

Platform:

GPL5949

11 Samples

Download data: PAIR

(Submitter supplied) Goal: To identify copy number variation in normal individuals using high density, non-polymorphic oligonucleotide probes Background DNA sequence diversity within the human genome may be more greatly affected by copy number variations (CNVs) than single nucleotide polymorphisms (SNPs). Although the importance of CNVs in genome wide association studies (GWAS) is becoming widely accepted, the optimal methods for identifying these variants are still under evaluation. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platforms:

GPL6660 GPL6659

42 Samples

Download data: CEL