GEO DataSets

(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) 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) 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:

GPL9866 GPL9865

90 Samples

Download data: PAIR, 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) 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) 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:

GPL9219 GPL9221 GPL9220

114 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) 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) 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:

GPL18174 GPL18175

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) 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) Background: The chicken (Gallus gallus) is an important model organism that bridges the evolutionary gap between mammals and other vertebrates. Copy number variations (CNVs) are a form of genomic structural variation widely distributed in the genome. CNV analysis has recently gained greater attention and momentum, as the identification of CNVs can contribute to a better understanding of traits important to both humans and other animals. more...

Organism:

Gallus gallus

Type:

Genome variation profiling by SNP array

Platform:

GPL18807

475 Samples

Download data

(Submitter supplied) Copy number variations (CNVs) are an important source of genomic structural variation, and can be used as markers to investigate phenotypic and economic traits. CNVs also have functional effects on gene expression and can contribute to disease susceptibility in mammals. Currently, single nucleotide polymorphism genotyping arrays (SNP chips) are the technology of choice for identifying CNV variations. more...

Organism:

Bos taurus

Type:

Genome variation profiling by SNP array; SNP genotyping by SNP array

Platform:

GPL18258

12 Samples

Download data: CEL, TXT

(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) Here we describe a genome-wide analysis of copy number variations (CNVs) in Chinese domestic cattle by using array comparative genomic hybridization (array CGH) and quantitative PCR (qPCR). We conducted array CGH analysis on 30 male cattle individuals, animals from consisting of 12 breeds of Bos taurus/Bos indicus, 1 Bos grunniens and and two ones of Bubalus bubalis breeds for with beef, and/or dairy or dual purpose. more...

Organism:

Bos grunniens; Bos taurus; Bubalus bubalis

Type:

Genome variation profiling by genome tiling array

Platform:

GPL17177

30 Samples

Download data: PAIR, TXT

(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) 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; Oryza sativa Indica Group; Oryza sativa Japonica Group

Type:

Genome variation profiling by genome tiling array

Platform:

GPL13842

21 Samples

Download data: PAIR, 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