GEO DataSets

(Submitter supplied) While nucleotide-resolution maps of genomic structural variants (SVs) have provided insights into the origin and impact on phenotypic diversity in humans, comparable maps in nonhuman primates have thus far been lacking. Using massively parallel DNA sequencing we constructed fine-resolution, species-specific structural variation and segmental duplication maps for five chimpanzees, five orang-utans, and five rhesus macaques. more...

Organism:

Pongo abelii; Macaca mulatta; Pan troglodytes; Pongo pygmaeus

Type:

Genome variation profiling by genome tiling array

30 related Platforms

30 Samples

Download data: TXT

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

Organism:

Pongo abelii; Macaca mulatta; Pan paniscus; Pongo pygmaeus pygmaeus; Homo sapiens; Pan troglodytes; Gorilla gorilla

Type:

Genome variation profiling by genome tiling array

Platforms:

GPL7749 GPL7748

47 Samples

Download data: PAIR

(Submitter supplied) Wilson and King were among the first to recognize that the extent of phenotypic change between humans and great apes was dissonant with the rate of molecular change. Proteins are virtually identical; cytogenetically there are few rearrangements that distinguish ape-human chromosomes; rates of single-basepair change and retroposon activity have slowed particularly within hominid lineages when compared to rodents or monkeys. more...

Organism:

Pongo abelii; Pan troglodytes; Pongo pygmaeus pygmaeus; Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platforms:

GPL7748 GPL7749

24 Samples

Download data: PAIR

(Submitter supplied) Wilson and King were among the first to recognize that the extent of phenotypic change between humans and great apes was dissonant with the rate of molecular change. Proteins are virtually identical; cytogenetically there are few rearrangements that distinguish ape-human chromosomes; rates of single-basepair change and retroposon activity have slowed particularly within hominid lineages when compared to rodents or monkeys. more...

Organism:

Pongo abelii; Macaca mulatta; Pan paniscus; Pongo pygmaeus pygmaeus; Homo sapiens; Pan troglodytes; Gorilla gorilla

Type:

Genome variation profiling by genome tiling array

Platforms:

GPL7749 GPL7748

23 Samples

Download data: PAIR

(Submitter supplied) Many loci in the human genome harbor complex genomic structures that can result in susceptibility to genomic rearrangements leading to various genomic disorders. Nephronophthisis 1 (NPHP1, MIM# 256100) is an autosomal recessive disorder that can be caused by defects of NPHP1; the gene maps within the human 2q13 region where low copy repeats (LCRs) are abundant. Loss of function of NPHP1 is responsible for approximately 85% of the NPHP1 cases - about 80% of such individuals carry a large recurrent homozygous NPHP1 deletion that occurs via non-allelic homologous recombination (NAHR) between two flanking directly oriented ~45 kb LCRs. more...

Organism:

Macaca mulatta; Gorilla gorilla; Pongo abelii; Homo sapiens; Papio anubis; Pan troglodytes

Type:

Genome variation profiling by genome tiling array

Platform:

GPL21019

32 Samples

Download data: TXT

(Submitter supplied) We synthesized the PAX8-NFE2L2 fusion transcript and cloned it into a lentiviral vector, and used this to overexpress it in the murine prostate adenocarcinoma cell line TRAMP-C1.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

7 Samples

Download data: TXT

(Submitter supplied) Intra-specific polymorphism in copy number is documented in many organisms, including human and chimpanzee, but very little is known for other great apes. This study aims to provide CNVs data for orangutan, gorilla, bonobo and chimpanzee, and compare the CNV patterns among these species, as well as with human CNVs and segmental duplications from public databases.

Organism:

Gorilla gorilla; Pongo pygmaeus; Pongo sp.; Homo sapiens; Gorilla gorilla gorilla; Pan paniscus; Pan troglodytes; Pongo abelii; Pan troglodytes troglodytes

Type:

Genome variation profiling by genome tiling array

Platform:

GPL7749

58 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 familiaris; Canis lupus

Type:

Genome variation profiling by genome tiling array

Platform:

GPL7501

19 Samples

Download data: PAIR, TXT

(Submitter supplied) Clarifying structural variants (SV) profiles in nonhuman primates could provide insights into the genetic background underlying human-specific traits, but such resources are largely lacking. Here, we report the largest SV atlas generated to date from a population of 1,026 macaques, verified by genome assembly for one of them. This accurate, quantitative map indicates stronger purifying selection on inversions located in regulatory regions, suggesting a strategy for prioritizing those with the most important functions. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28457

4 Samples

Download data: MTX, TSV

(Submitter supplied) Structural variation (SV) is a class of genetic variants involving long stretches of DNA and provides substantial innovations for adaptation and evolution. Investigation of SV profiles and turnover in nonhuman primates can help answer fundamental questions, such as what makes us uniquely human. Here, we present the high-resolution comparative 3D genome organizations of prefrontal cortex (PFC) of adult human and rhesus macaque. more...

Organism:

Macaca mulatta; Homo sapiens

Type:

Other

Platforms:

GPL27943 GPL24676

2 Samples

Download data: BED, BEDPE