GEO DataSets

(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:

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

Type:

Methylation profiling by array

Platform:

GPL13534

32 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:

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

Type:

Genome variation profiling by genome tiling array

Platform:

GPL7749

58 Samples

Download data: PAIR, 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) DNA methylation in sperm is among the most important factors shaping evolution of the mammalian genome. By directly altering germline mutation rates, the DNA methylation system has shaped the CpG landscape of mammalian genomes, resulting in the CpG island phenomenon. Yet little is known about how this system itself has co-evolved with its substrate during mammalian evolution. We analyzed full-genome single-CpG DNA methylation profiles in sperm from human, chimp, gorilla, rhesus, mouse, rat and dog. more...

Organism:

Canis lupus familiaris; Gorilla gorilla; Rattus norvegicus

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL18694 GPL16540 GPL21650

12 Samples

Download data: TXT

(Submitter supplied) We have determined methylation state differences in the epigenomes of neutrophils purified from human and chimpanzee. We used deep sequencing of ends generated by digestion with a methylation-sensitive restriction enzyme, followed by analysis with the MetMap computational pipeline to infer methylation states from the sequencing data. Using the orangutan as an outgroup, analysis of DNA sequence substitutions in CG-dense regions that are either methylated or unmethylated in all three species indicates that methylation states in the neutrophil reflect methylation states in the germline. more...

Organism:

Homo sapiens; Pan troglodytes; Pongo pygmaeus

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL10547 GPL10548 GPL9052

11 Samples

Download data: TXT, WIG

(Submitter supplied) We compared the genome-wide patterns of DNA methylation in the brains of humans to those of our closest evolutionary relative, chimpanzees, using base-pair resolution whole-genome methylation maps of the prefrontal cortex. Our data reveal that the prefrontal cortex is the most heavily methylated among the human tissues examined so far. Nevertheless, hundreds of genes exhibit dramatically reduced levels of promoter DNA methylation in the human brain relative to the chimpanzee brain. more...

Organism:

Pan troglodytes; Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL15434 GPL9115 GPL15433

6 Samples

Download data: GFF

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

Organism:

Macaca mulatta; Homo sapiens; Pan troglodytes

Type:

Expression profiling by array; Expression profiling by high throughput sequencing

5 related Platforms

92 Samples

Download data: CEL, TXT

(Submitter supplied) We identified human-specific gene expression patterns in the brain by comparing expression with chimpanzee and rhesus macaque.

Organism:

Pan troglodytes; Macaca mulatta; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL9378 GPL9115 GPL9160

44 Samples

Download data: TXT

(Submitter supplied) We identified human-specific gene expression patterns in the brain by comparing expression with chimpanzee and rhesus macaque

Organism:

Pan troglodytes; Macaca mulatta; Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL570 GPL3535

48 Samples

Download data: CEL, TXT

(Submitter supplied) Genome-wide prefrontal cortex and cerebellum DNA methylation profiles of younger and older adult humans, captive chimpanzees, and captive rhesus macaques

Organism:

Macaca mulatta; Homo sapiens; Pan troglodytes

Type:

Methylation profiling by array

Platform:

GPL23976

44 Samples

Download data: IDAT

(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 troglodytes; Pan paniscus; Homo sapiens

Type:

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

Platforms:

GPL16809 GPL11154 GPL17238

18 Samples

Download data: 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:

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

Type:

Genome binding/occupancy profiling by high throughput sequencing

7 related Platforms

15 Samples

Download data: BED

(Submitter supplied) It has long been hypothesized that changes in gene regulation have played an important role in primate evolution. However, despite the wealth of comparative gene expression data, there are still only few studies that focus on the mechanisms underlying inter-primate differences in gene regulation. In particular, we know relatively little about the degree to which changes in epigenetic profiles might explain differences in gene expression levels between primates. more...

Organism:

Pan troglodytes; Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL8490

71 Samples

Download data: TXT

(Submitter supplied) We couple long-read sequence assembly, full-length cDNA sequencing, and a multi-platform scaffolding approach to produce ab initio chimpanzee and orangutan genome assemblies where most genes are complete, gaps are closed, and novel gene models are identified. We further analyzed the overlap between structural variants in the human genome and gene expression differences in human and chimpanzee cells, including iPS-derived organoid radial glia cells.

Organism:

Pan troglodytes; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL16791 GPL19148

117 Samples

Download data: TXT

(Submitter supplied) Genome wide DNA methylation profiling of captive chimpanzees of ages spanning the chimpanzee lifespan (whole blood) Methylation levels have been shown to change with age at sites across the human genome. Change at some of these sites is so consistent across individuals that it can be used as an “epigenetic clock” to predict an individual’s chronological age within a few years. Studies of age-related epigenetic change in other mammals, including mice, whales, and canids, show that some but not all of the same loci as in humans undergo age-associated methylation changes. more...

Organism:

Pan troglodytes; Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL21145

113 Samples

Download data: CSV, IDAT

(Submitter supplied) Accelerated brain development is a unique feature of the human species. Not only the size but also morphology, in particular the connections between frontal cortex and basal ganglia distinguish the human brain from great apes and other primates. Recent findings suggest that structural features which may be important for language acquisition are influenced by FOXP2, key regulator of CNTNAP2. CNTNAP2 is one of the largest genes in the chimpanzee genome, encompassing 2.5 Mb. more...

Organism:

Pan troglodytes

Type:

Methylation profiling by genome tiling array

Platform:

GPL18022

5 Samples

Download data: PAIR

(Submitter supplied) Accelerated brain development is a unique feature of the human species. Not only the size but also morphology, in particular the connections between frontal cortex and basal ganglia distinguish the human brain from great apes and other primates. Recent findings suggest that structural features which may be important for language acquisition are influenced by FOXP2, key regulator of CNTNAP2. CNTNAP2 is one of the largest genes in the human genome, encompassing 2.3 Mb. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL18021

6 Samples

Download data: PAIR