GEO DataSets

(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) 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:

GPL17150

12 Samples

Download data: PAIR

(Submitter supplied) A CNV map in pigs could facilitate the identification of chromosomal regions that segregate for important economic and disease phenotypes. The goal of this study was to identify CNV regions (CNVRs) in pigs based on a custom array comparative genome hybridization (aCGH). We carried out a custom-made array comparative genome hybridization (aCGH) experiment in order to identify copy number variations (CNVs) in the pig genome analysing animals of diverse pig breeds (White Duroc, Yangxin, Erhualian, Tongcheng, Large White, Pietrain, Landrace and Chinese new pig line DIV ) using a tiling oligonucleotide array with ~720,000 probes designed on the pig genome (Sus scrofa genome version 9.0).

Organism:

Sus scrofa

Type:

Genome variation profiling by genome tiling array

Platform:

GPL16165

12 Samples

Download data: PAIR

(Submitter supplied) Genome-wide SNP genotyping array can genotyped SNP highthroughly. It can be used in many aspects, such as phylogeny relationships, genome-wide association studies, copy number identification.

Organism:

Sus scrofa

Type:

SNP genotyping by SNP array

Platform:

GPL11379

14 Samples

Download data: TXT

(Submitter supplied) CNV plays an important role in the chicken genomic studies,it is imperative need to investigate the extent and pattern of CNVs using array comparative genomic hybridization (aCGH) in chinese chicken breeds for future studies associating phenotype to genome architecture. we describe systematic and genome-wide analysis of CNVs loci in five Chinese indigenous chicken breeds were evaluated by aCGH.

Organism:

Gallus gallus

Type:

Genome variation profiling by genome tiling array

Platform:

GPL9799

10 Samples

Download data: PAIR

(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) 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) Investigating genome-wide characteristics of CNVs in 6 horses representing 6 distinct breeds by using the aCGH method and performed GO and KEGG analysis for the CNVs genes.This result is an important complement to the mapping of horse whole-genome CNVs and helpful to study plateau horses’ adaption to the plateau’s environment.

Organism:

Equus caballus

Type:

Genome variation profiling by genome tiling array

Platform:

GPL17952

6 Samples

Download data: PAIR

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

Organism:

Gallus gallus

Type:

Genome variation profiling by genome tiling array

Platforms:

GPL18175 GPL18174

11 Samples

Download data: PAIR, TXT

(Submitter supplied) Copy number variation (CNV) is important and widespread in the genome, and is a major cause of disease and phenotypic diversity. Herein, we perform a genome-wide analysis of CNVs in the 12 diversified chicken genomes based on next-generation sequencing. We apply aCGH experiments to confirm our predicted CNVs. Results from aCGH agree well with our findings and the Pearson’s correlation values between the test and reference samples range from 0.644 to 0.722.

Organism:

Gallus gallus

Type:

Genome variation profiling by genome tiling array

Platform:

GPL18175

3 Samples

Download data: TXT

(Submitter supplied) Copy number variation (CNV) is important and widespread in the genome, and is a major cause of disease and phenotypic diversity. Herein, we perform a genome-wide analysis of CNVs in the 12 diversified chicken genomes based on next-generation sequencing. We apply aCGH experiments to confirm our predicted CNVs. Results from aCGH agree well with our findings and the Pearson’s correlation values between the test and reference samples range from 0.395 to 0.740.

Organism:

Gallus gallus

Type:

Genome variation profiling by genome tiling array

Platform:

GPL18174

8 Samples

Download data: PAIR

(Submitter supplied) We carried out a cross species cattle-sheep array comparative genome hybridization (aCGH) experiment in order to identify copy number variations (CNVs) in the sheep genome analysing animals of Italian dairy breeds (Sarda, Bagnolese, Laticauda, Massese and Valle del Belice) using a tiling oligonucleotide array with ~385,000 probes designed on the bovine genome. We identified 135 CNV regions (CNVRs) covering about 10.5 Mb of the virtual sheep genome referred to the bovine genome (0.398%) with a mean and median equal to 77.6 kb and 55.9 kb, respectively. more...

Organism:

Bos taurus; Ovis aries

Type:

Genome variation profiling by genome tiling array

Platform:

GPL10990

11 Samples

Download data: PAIR

(Submitter supplied) Recents studies in mammalian genomes have uncovered the extent of copy number variation (CNV) that contributes to phenotypic diversity, including health and disease status. Here we report the first glimpse of CNVs in the pig genome covering part of the chromosomes 4, 7, 14 and 17 already sequenced and assembled. We used a custom tiling oligonucleotide array with a median probe spacing of 409 bp to screen 12 unrelated Duroc boar founders of a vast-family material. more...

Organism:

Sus scrofa

Type:

Genome variation profiling by genome tiling array

Platform:

GPL6553

24 Samples

Download data: PAIR

(Submitter supplied) 38 horses from 16 diverse breeds and Przewalski's Horse were used to generate a composite CNV map of equine genome. This map was used to detect novel copy number variation in six horses affected with disorder of sexual development (DSD).

Organism:

Equus caballus

Type:

Genome variation profiling by array

Platform:

GPL18315

44 Samples

Download data: TXT

(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) Copy number variation profiles comparing control female Dehong chicken blood DNA with 3 different chicken breeds (white Leghorn, Cobb broiler, and Dou chicken) blood DNA. Each test breed had one male and one female sample, for a total of 6 test DNA samples. The goal is to determine the global copy number variation profiles between chicken breeds.

Organism:

Gallus gallus

Type:

Genome variation profiling by genome tiling array

Platform:

GPL13398

6 Samples

Download data: TXT

(Submitter supplied) Background: Detecting genetic variation is a critical step in elucidating the molecular mechanisms underlying phenotypic diversity. Until recently, such detection has mostly focused on single nucleotide polymorphisms (SNPs) because of the ease in screening complete genomes. Another type of variant, copy number variation (CNV), is emerging as a significant contributor to phenotypic variation in many species. more...

Organism:

Gallus gallus

Type:

Genome variation profiling by genome tiling array

Platform:

GPL15501

62 Samples

Download data: TXT

(Submitter supplied) Structural and functional impacts of copy number variations (CNVs) on livestock genomes are not yet well understood. In this study, we have identified 1853 CNV regions (CNVRs) using population-scale sequencing data generated from 75 cattle of 8 breeds (Holstein, Angus, Jersey, Limousin, Romagnola, Brahman, Gir and Nelore). Individual genome sequence coverage ranged from 4 to 30 fold, with a mean of 11.8 fold. more...

Organism:

Bos taurus

Type:

Genome variation profiling by genome tiling array

Platform:

GPL11314

25 Samples

Download data: BED, PAIR

(Submitter supplied) Copy number variation (CNV) is an important type of genetic variation contributing to phenotypic differences among mammals. Up to now, GWAS analysis using CNV called by array CGH is lacking in livestock like Holstein cattle. The objectives of this work are to identify CNVs using high-density aCGH data and explore functional CNVs which are associated with complex traits by GWAS method in Holstein cattle. more...

Organism:

Bos taurus

Type:

Genome variation profiling by genome tiling array; Third-party reanalysis

Platform:

GPL11314

41 Samples

Download data: PAIR

(Submitter supplied) We describe a more detailed survey undertaken to detect candidate CNVs in a panel of 20 Asian cultivated rice and the genome-wide characteristics of CNVs in subspecies and groups. These resources allowed us to analyze genetic structure as indicated by CNVs, to implicate the biological roles of CNVs, and to identify candidate CNVs that are likely to occur independently in groups and contribute to differences between the subspecies.

Organism:

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

Type:

Genome variation profiling by genome tiling array

Platform:

GPL13842

21 Samples

Download data: PAIR, TXT