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Links from GEO DataSets

Items: 20

1.

Next generation sequencing reveals the diversity and population-genetic properties of cattle CNVs

(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
Series
Accession:
GSE62990
ID:
200062990
2.

Copy number variation of individual cattle genomes using next-generation sequencing.

(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
Series
Accession:
GSE31018
ID:
200031018
3.

Analysis of copy number variations among diverse cattle breeds

(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
Series
Accession:
GSE19866
ID:
200019866
4.

Identification of copy number variation using aCGH in Chinese chicken breeds

(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
Series
Accession:
GSE49889
ID:
200049889
5.

Validation experiment of copy number variations identified by next-generation sequencing in chickens

(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
Series
Accession:
GSE54119
ID:
200054119
6.

Validation experiment of copy number variations identified by next-generation sequencing in chickens (part 2)

(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
Series
Accession:
GSE54118
ID:
200054118
7.

Validation experiment of copy number variations identified by next-generation sequencing in chickens (part 1)

(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
Series
Accession:
GSE54117
ID:
200054117
8.

CGH analyses for the Chinese indigenous pig breeds and commercial pig breeds [Agilent]

(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
Series
Accession:
GSE49299
ID:
200049299
9.

244K array Comparative Genomic Hybridization for the characterization of CNVs among inbred Fayoumi, inbred Leghorn, Line A broiler, and Line B broiler chicken

(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
Series
Accession:
GSE44440
ID:
200044440
10.

Computational detection and experimental validation of segmental duplications and associated copy number variants in river buffalo (Bubalus bubalis)

(Submitter supplied) Duplicated sequences are the important source of gene innovation and structural variation within mammalian genomes. Using a read depth approach based on next-generation sequencing, we performed a genome-wide analysis of segmental duplications (SDs) and associated copy number variants (CNVs) in water buffalo (Bubalus bubalis). Aligning to the UMD3.1 cattle genome, we estimated 44.6 Mb (~1.73% of cattle genome) segmental duplications in the autosomes and X chromosome using the sequencing reads of Olimpia (the sequenced water buffalo). more...
Organism:
Bubalus bubalis
Type:
Genome variation profiling by genome tiling array
Platform:
GPL25422
14 Samples
Download data: TXT
Series
Accession:
GSE118117
ID:
200118117
11.

Genome-Wide Detection of CNVs and Their Association with Complex Traits in Holsteins

(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
Series
Accession:
GSE122478
ID:
200122478
12.

Genome-wide detection by array CGH of copy number variations among diverse horse breeds

(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
Series
Accession:
GSE52504
ID:
200052504
13.

Genome-wide identification of copy number variations in Holstein cattle from Baja California, Mexico, using high-density SNP genotyping arrays

(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
Series
Accession:
GSE54813
ID:
200054813
14.

Population Structure, and Selection Signatures underlying High-Altitude Adaptation Inferred from Genome-Wide Copy Number Variations in Chinese Indigenous Cattle

(Submitter supplied) Copy number variations (CNVs) have been demonstrated as crucial substrates for evolution, adaptation and breed formation. Chinese indigenous cattle breeds exhibit a broad geographical distribution and diverse environmental adaptability. Here, we analyzed the population structure and adaptation to high altitude of Chinese indigenous cattle based on genome-wide CNVs derived from the high-density BovineHD SNP array. more...
Organism:
Bos indicus; Bos grunniens; Bos taurus
Type:
Genome variation profiling by SNP array
Platform:
GPL21267
355 Samples
Download data: IDAT, TXT
Series
Accession:
GSE142218
ID:
200142218
15.

Copy number variation in the bovine genome

(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 GPL9219 GPL9221
114 Samples
Download data: PAIR
Series
Accession:
GSE18174
ID:
200018174
16.

Analysis of copy number variations among Chinese cattle breeds

(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:
Bubalus bubalis; Bos taurus; Bos grunniens
Type:
Genome variation profiling by genome tiling array
Platform:
GPL17177
30 Samples
Download data: PAIR, TXT
Series
Accession:
GSE47086
ID:
200047086
17.

Large scale variation in copy number in chicken breeds

(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
Series
Accession:
GSE47623
ID:
200047623
18.

CGH analyses for the Chinese indigenous pig breeds and commercial pig breeds

(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
Series
Accession:
GSE46847
ID:
200046847
19.

Genome-wide copy number variant discovery in dogs using the CanineHD genotyping array

(Submitter supplied) This study used the CanineHD genotyping array to investigate copy number variants in the dog genome in a total of 351 samples from 30 different breeds.
Organism:
Canis lupus familiaris
Type:
Genome variation profiling by SNP array; SNP genotyping by SNP array
Platform:
GPL17481
351 Samples
Download data: TXT
Series
Accession:
GSE55134
ID:
200055134
20.

A first comparative map of copy number variations in the sheep genome

(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
Series
Accession:
GSE25122
ID:
200025122
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