GEO DataSets

(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:

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

Type:

Genome variation profiling by genome tiling array

Platform:

GPL7749

58 Samples

Download data: PAIR, TXT

(Submitter supplied) Structural variation has played an important role in the evolutionary restructuring of human and great ape genomes. We generated approximately 10-fold genomic sequence coverage from a western lowland gorilla and integrated these data into a physical and cytogenetic framework to develop a comprehensive view of structural variation. We discovered and validated over 7,665 structural changes within the gorilla lineage including sequence resolution of inversions, deletions, duplications and retrotranspositions. more...

Organism:

Homo sapiens; Pan troglodytes; Gorilla gorilla

Type:

Genome variation profiling by genome tiling array

Platforms:

GPL11674 GPL9684

7 Samples

Download data: PAIR

(Submitter supplied) DNA methylation is an epigenetic modification involved in regulatory processes such as cell differentiation during development, X-chromosome inactivation, genomic imprinting and susceptibility to complex diseases. These changes can be inherited through generations and likely have played an important role during human evolution. We performed a comparative analysis of CpG methylation patterns between humans and all great apes (chimpanzee, bonobo, gorilla and orangutan) on a total of 32 individuals.Our analysis identified ~1,000 genes with significantly altered methylation patterns among the great apes, including ~200 with a methylation pattern unique to humans. more...

Organism:

Pongo pygmaeus; Homo sapiens; Pan troglodytes verus; Gorilla gorilla gorilla; Pongo abelii; Gorilla beringei graueri; Pan paniscus; Pan troglodytes schweinfurthii; Pan troglodytes troglodytes

Type:

Methylation profiling by array

Platform:

GPL13534

32 Samples

Download data: TXT

(Submitter supplied) Data from gorilla fibroblast cell lines described in Genome Research paper "Comparative analysis of gene expression patterns in human and African great ape cultured fibroblasts" Keywords = African Great Ape, Human Evolution, Fibroblast, Bonobo, Gorilla, Human Keywords: ordered

Organism:

Gorilla gorilla; Homo sapiens

Type:

Expression profiling by array

Platform:

GPL8300

12 Samples

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(Submitter supplied) Data from bonobo fibroblast cell lines described in Genome Research paper "Comparative analysis of gene expression patterns in human and African great ape cultured fibroblasts" Keywords = African Great Ape, Human Evolution, Fibroblast, Bonobo, Gorilla, Human Keywords: ordered

Organism:

Pan paniscus; Homo sapiens

Type:

Expression profiling by array

Platform:

GPL8300

11 Samples

Download data

(Submitter supplied) Data from human fibroblast cell lines described in Genome Research paper "Comparative analysis of gene expression patterns in human and African great ape cultured fibroblasts" Keywords = African Great Ape, Human Evolution, Fibroblast, Bonobo, Gorilla, Human Keywords: ordered

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL8300

23 Samples

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(Submitter supplied) Data files from Genome Research paper "Comparative analysis of gene expression patterns in human and African great ape cultured fibroblasts" Keywords = African Great Ape, Human Evolution, Fibroblast, Bonobo, Gorilla, Human Keywords: other

Organism:

Pan paniscus; Gorilla gorilla; Homo sapiens

Type:

Expression profiling by array

Platform:

GPL8300

46 Samples

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(Submitter supplied) Sixteen individual rhesus macaque genomes were compared to a reference macaque genome (R354) on custom-designed sure-print 1M oligonucleotide microarray Agilent (Agilent Technologies) aCGH slide per manufacturer’s recommendations.

Organism:

Macaca mulatta

Type:

Genome variation profiling by genome tiling array

Platform:

GPL9903

17 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) Understanding evolutionary mechanisms underlying expansion and reorganization of the human brain represents an important aspect in analyzing the emergence of cognitive abilities typical of our species. Comparative analyses of neuronal phenotypes in closest living relatives (Pan troglodytes; the common chimpanzee) can shed the light into changes in neuronal morphology compared to the last common ancestor (LCA), opening possibilities for analyses of the timing of their appearance, and the role of evolutionary mechanisms favoring a particular type of information processing in humans. more...

Organism:

Pan troglodytes; Homo sapiens

Type:

Expression profiling by high throughput sequencing

4 related Platforms

12 Samples

Download data: TXT

(Submitter supplied) Understanding cellular and molecular differences between human and non-human primates (NHPs) is essential to the basic comprehension of the evolution and diversity of our own species. Until now, preserved tissues have been the main source of most comparative studies between humans, chimpanzees (Pan troglodytes) and bonobos (Pan paniscus). However, these tissue samples do not fairly represent the distinctive traits of live cell behavior, are not amenable to genetic manipulation and do not allow translation of observed differences into phenotypical divergence. more...

Organism:

Pan paniscus; Homo sapiens; Pan troglodytes

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL11154 GPL16809 GPL17238

18 Samples

Download data: 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) This SuperSeries is composed of the SubSeries listed below.

Organism:

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

Type:

Genome variation profiling by genome tiling array

Platforms:

GPL7748 GPL7749

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:

Pan troglodytes; Pongo abelii; 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:

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

Type:

Genome variation profiling by genome tiling array

Platforms:

GPL7748 GPL7749

23 Samples

Download data: PAIR

(Submitter supplied) The great tit is a widely studied passerine bird species in ecology that, in the past decades, has provided important insights into speciation, phenology, behavior and microevolution. After completion of the great tit genome sequence, a customized high density 650k SNP array was developed enabling more detailed genomic studies in this species.

Organism:

Parus major

Type:

Genome variation profiling by SNP array

Platform:

GPL24144

3116 Samples

Download data: CEL, TXT

(Submitter supplied) Evolution of transcriptional regulation is thought to be a major cause of the evolution of phenotypic traits. We compared DNase I Hypersensitive sites in fibroblast cells from five primates (human, chimpanzee, gorilla, orangutan, and macaque). We identified approximately 90,000 DHS sites, of which 59% are not significantly different between species, 27% are differential and likely due to a single evolutionary change, and 14% are differential and likely due to multiple changes. more...

Organism:

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

Type:

Genome binding/occupancy profiling by high throughput sequencing

7 related Platforms

15 Samples

Download data: BED

(Submitter supplied) This study used the NimbleGen dog whole genome CGH 2.1M tiling array to assay copy number variants in the dog genome in multiple breeds and wolf.

Organism:

Canis lupus; Canis lupus familiaris

Type:

Genome variation profiling by genome tiling array

Platform:

GPL11335

53 Samples

Download data: PAIR

(Submitter supplied) This study used two different NimbleGen platforms to identify canine CNVs. The first identifies genome-wide CNVs while the second genotypes all known canine CNVs in a large panel of dogs from multiple breeds.

Organism:

Canis lupus familiaris; Canis lupus

Type:

Genome variation profiling by genome tiling array

Platforms:

GPL11335 GPL11333

75 Samples

Download data: PAIR

(Submitter supplied) Bru-seq nascent RNA sequencing (PubMed ID 23973811) was performed on two primary human fibroblast cell lines, mouse embryonic stem cells, and GM12878 human lymphoblastoid cells. Read data, which include both exon and intron signals, were used to identify transcription unit spans genome-wide, where a transcription unit is roughly correspondent to the longest expressed isoform of a gene. However, because algorithms were not constrained by annotated genes, transcription units need not and often do not correspond precisely to gene boundaries and include extragenic transcription. more...

Organism:

Mus musculus; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL13112 GPL11154

8 Samples

Download data: BED