GEO DataSets

(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:

Homo sapiens; Pan troglodytes

Type:

Methylation profiling by array

Platform:

GPL8490

71 Samples

Download data: TXT

(Submitter supplied) A long-standing hypothesis is that changes in gene regulation play an important role in adaptive evolution, notably in primates. Yet, in spite of the evidence accumulated in the past decade that regulatory changes contribute to many species-specific adaptations, we still know remarkably little about the mechanisms of regulatory evolu tion. In this study we focused on DNA methylation, an epigenetic mechanism whose contribution to the evolution of gene expression remains unclear. more...

Organism:

Macaca mulatta; Pan troglodytes; Homo sapiens

Type:

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

Platforms:

GPL16791 GPL19148 GPL19129

159 Samples

Download data: RDA, 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:

Homo sapiens; Pan troglodytes

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL9115 GPL15434 GPL15433

6 Samples

Download data: GFF

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

Organism:

Pan troglodytes; Macaca mulatta; Homo sapiens

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:

Macaca mulatta; Homo sapiens; Pan troglodytes

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:

Homo sapiens; Macaca mulatta; Pan troglodytes

Type:

Expression profiling by array

Platforms:

GPL570 GPL3535

48 Samples

Download data: CEL, 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

(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:

Pan troglodytes; Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL9378 GPL9115

4 Samples

Download data: BED, BEDGRAPH

(Submitter supplied) Regulatory changes have long been hypothesized to play an important role in primate evolution. To identify adaptive regulatory changes in humans, we performed a genome-wide survey for genes whose regulation evolves under natural selection. To do so, we used a novel multi-species microarray to measure gene expression levels in livers, kidneys, and hearts from six humans, chimpanzees, and rhesus macaques. more...

Organism:

Macaca mulatta; Homo sapiens; Pan troglodytes

Type:

Expression profiling by genome tiling array

Platform:

GPL6898

108 Samples

Download data: TXT

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

Organism:

Homo sapiens; Macaca mulatta

Type:

Methylation profiling by genome tiling array

Platforms:

GPL13216 GPL9448

6 Samples

Download data: PAIR

(Submitter supplied) The highly improved cognitive function is the most significant change in human evolutionary history. Recently, several large-scale studies reported the evolutionary roles of DNA methylation; however, the role of DNA methylation on brain evolution is largely unknown. To test if DNA methylation has contributed to the evolution of human brain, with the use of MeDIP-Chip and SEQUENOM MassARRAY, we conducted a genome-wide analysis to identify differentially methylated regions (DMRs) in the brain between humans and rhesus macaques. more...

Organism:

Macaca mulatta

Type:

Methylation profiling by genome tiling array

Platform:

GPL13216

3 Samples

Download data: PAIR

(Submitter supplied) The highly improved cognitive function is the most significant change in human evolutionary history. Recently, several large-scale studies reported the evolutionary roles of DNA methylation; however, the role of DNA methylation on brain evolution is largely unknown. To test if DNA methylation has contributed to the evolution of human brain, with the use of MeDIP-Chip and SEQUENOM MassARRAY, we conducted a genome-wide analysis to identify differentially methylated regions (DMRs) in the brain between humans and rhesus macaques. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL9448

3 Samples

Download data: PAIR

(Submitter supplied) Differences in gene regulation contribute to phenotypic differences between humans and other primates. While co-transcriptional gene regulatory mechanisms such as alternative polyadenylation (APA) can help explain how variation in gene regulation manifests, such mechanisms remain understudied. We measured polyadenylation site (PAS) usage in a panel of 6 human and 6 chimpanzee lymphoblastoid cell lines (LCLs). more...

Organism:

Homo sapiens; Pan troglodytes

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL20301 GPL18573 GPL21121

23 Samples

Download data: BED, 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) Using reduced representation bisulfite sequencing (RRBS), we have compared the methylomes of neuronal and non-neuronal cells from three female human and three chimpanzee cortices (Brodmann area 10). Differentially methylated regions (DMRs) with genome-wide significance were enriched in specific chromosomal regions. Intraspecific methylation differences between neuronal and non-neuronal cells were approximately three times more abundant than interspecific methylation differences between human and chimpanzee cell types. more...

Organism:

Homo sapiens; Pan troglodytes

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL9378 GPL9115

12 Samples

Download data: CSV

(Submitter supplied) Inter-individual variation in gene regulation has been shown to be heritable and it is quite often associated with differences in disease susceptibility between individuals. While many human studies focused on mapping associations between genetic and gene regulatory variation, much less attention has been paid to the evolutionary processes that shape the observed differences in gene regulation between individuals in humans or any other primate. more...

Organism:

Pan troglodytes

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23423

38 Samples

Download data: TSV

(Submitter supplied) To study regulatory differences between species, the field of comparative primate genomics has used several approaches, including the use of post mortem frozen tissues, cell lines, and model organisms. However, there are limited quality cell lines from primates and post-mortem tissues cannot be staged, are not amenable to experimental perturbations and are often subject to high environmental variances. more...

Organism:

Homo sapiens; Pan troglodytes

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL20301 GPL23423

211 Samples

Download data: CSV

(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:

Pan troglodytes; Pongo pygmaeus; Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL10548 GPL10547 GPL9052

11 Samples

Download data: TXT, WIG