GEO DataSets

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

Organism:

Macaca mulatta; Pan troglodytes; Homo sapiens; Hoolock leuconedys; Macaca; Macaca fascicularis

Type:

Genome variation profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

6 related Platforms

86 Samples

Download data

(Submitter supplied) We report the application of DNA sequencing technology for high-throughput sequencing of mix candidate genes' PCR products totally 38 based on DNA from human, chimpanzee, gibbon, macaque and crab eating macaque profrontal cortex tissues.

Organism:

Pan troglodytes; Homo sapiens; Hoolock leuconedys; Macaca; Macaca fascicularis

Type:

Genome variation profiling by high throughput sequencing

5 related Platforms

48 Samples

Download data: VCF

(Submitter supplied) To gain further insights into human brain specific epigenetic changes, we generated whole genome bisulfite sequencing methylation maps (methylomes) of rhesus macaque brains. These were then compared to methylomes of human and chimpanzee brains that were previously generated. We then performed validation experiments using targeted bisulfite sequencing. 

Organism:

Macaca mulatta

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL14954

2 Samples

Download data: BED

(Submitter supplied) We report the application of DNA sequencing technology for high-throughput sequencing of mix bis-PCR products totally 38 based on bisulfate treated DNA from human, chimpanzee, gibbon, macaque and crab eating macaque profrontal cortex tissues.

Organism:

Hoolock leuconedys; Macaca fascicularis; Pan troglodytes; Macaca mulatta; Homo sapiens

Type:

Methylation profiling by high throughput sequencing

5 related Platforms

38 Samples

Download data: TXT

(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) Recent discussions of human brain evolution have largely focused on increased neuron numbers and changes in their connectivity and expression. However, it is increasingly appreciated that oligodendrocytes play important roles in cognitive function and disease. Whether both cell types follow distinctive evolutionary trajectories is not known. We examined the transcriptomes of neurons and oligodendrocytes in the frontal cortex of humans, chimpanzees, and rhesus macaques. more...

Organism:

Pan troglodytes; Macaca mulatta; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL18573 GPL21120 GPL21121

95 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing; Other

Platforms:

GPL18573 GPL20795 GPL16791

245 Samples

Download data: TXT

(Submitter supplied) We carried out whole genome sequencing of 29 schizophrenia patients and 25 control individuals

Organism:

Homo sapiens

Type:

Other

Platforms:

GPL20795 GPL16791

54 Samples

Download data: BED, BIM, FAM

(Submitter supplied) We carried out cell-type specific whole genome bisulfite sequencing from BA46 that underwent fluorescence-activated nuclei sorting (FANS).

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL16791 GPL20795

95 Samples

Download data: TXT

(Submitter supplied) To address the heterogeneity of gene regulation and expression in cell types of a brain region with strong evidence for relevance to schizophrenia, we carried out whole genome methylation and expression analyses using post-mortem brain tissue from BA46 that underwent fluorescence-activated nuclei sorting (FANS). Importantly, we used whole genome bisulfite sequencing (WGBS) for methylation quantification to have an unbiased assessment of epigenetic modifications associated with schizophrenia, and additionally carried out whole genome sequencing (WGS) of the brain samples to account for genetic background differences. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

96 Samples

Download data: 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:

Pan troglodytes; Macaca mulatta; Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL23976

44 Samples

Download data: IDAT

(Submitter supplied) Complete genome sequencing has identified millions of DNA changes that differ between humans and chimpanzees. Although a subset of these changes likely underlies important phenotypic differences between humans and chimpanzees, it is currently difficult to distinguish causal from incidental changes and to map specific phenotypes to particular genome locations. To facilitate further genetic study of human-chimpanzee divergence, we have generated human and chimpanzee auto-tetraploids and allo-tetraploids by fusing induced pluripotent stem cells (iPSCs) of each species. more...

Organism:

Pan troglodytes; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL23423 GPL20301 GPL27803

69 Samples

Download data: GTF, TXT

(Submitter supplied) During germ cell and preimplantation development, mammalian cells undergo nearly complete reprogramming of DNA methylation patterns. We profiled the methylomes of human and chimp sperm as a basis for comparison to methylation patterns of ES cells. While the majority of promoters escape methylation in both ES cells and sperm, the corresponding hypomethylated regions show substantial structural differences. more...

Organism:

Homo sapiens; Pan troglodytes

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL9378 GPL9115

4 Samples

Download data: BED, BEDGRAPH

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

Type:

Methylation profiling by array

Platform:

GPL13534

32 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:

Homo sapiens; Pan troglodytes

Type:

Methylation profiling by genome tiling array

Platform:

GPL21145

113 Samples

Download data: CSV, IDAT

(Submitter supplied) Mutations in FOXP2, a member of the forkhead family of transcription factors, are the only known cause of developmental speech and language disorders in humans. To date, there are no known targets of human FOXP2 in the nervous system. The identification of FOXP2 targets in the developing human brain therefore provides a unique tool with which to explore the development of human language and speech. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL5630

8 Samples

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