GEO DataSets

(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:

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

Type:

Genome variation profiling by high throughput sequencing

5 related Platforms

48 Samples

Download data: VCF

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

Organism:

Hoolock leuconedys; Macaca mulatta; Pan troglodytes; Homo sapiens; 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) 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:

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

Type:

Methylation profiling by high throughput sequencing

5 related Platforms

38 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:

GPL9448 GPL13216

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) 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:

GPL15434 GPL9115 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) 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) While genome sequencing has identified numerous non-coding alterations between primate species, which of these are regulatory and potentially relevant to the evolution of the human brain is unclear. Here, we annotate cis-regulatory elements (CREs) in the human, rhesus macaque and chimpanzee genome using ChIP-sequencing in different anatomical parts of the adult brain. We find high similarity in the genomic positioning of CREs between rhesus macaque and humans, suggesting that the majority of these elements were already present in a common ancestor 25 million years ago. more...

Organism:

Pan troglodytes; Macaca mulatta; Homo sapiens; Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

8 related Platforms

98 Samples

Download data: BEDGRAPH, BW, NARROWPEAK, 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) 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:

Gorilla gorilla; Rattus norvegicus; Canis lupus familiaris

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL18694 GPL16540 GPL21650

12 Samples

Download data: TXT

(Submitter supplied) Here we provided the first single-base resolution DNA methylatome in chicken lungs by whole-genome bisulfite sequencing (MethylC-seq). In addition, two genetically distinct highly inbred chicken lines, Leghorn and Fayoumi, were used to examine how DNA methylation regulates mRNA gene expression between two lines. The methylation profile demonstrated that methylcytosines in the chicken were more likely to occur in CG dinucleotides than in non-CG sites. more...

Organism:

Gallus gallus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL9385

2 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

Expression profiling by array; Methylation profiling by genome tiling array

Platforms:

GPL13534 GPL10558

48 Samples

Download data

(Submitter supplied) DNA methylation has an impact on regulation of gene expression, however the relation between the two is complex. By performing an integrative analysis of the methylome and transcriptome of the four main circulating immune cell-subsets from healthy females, namely B cells, monocytes, CD4 and CD8 T cells, the relation between the two was characterized. In addition, in light of the known sex bias in the prevalence of several immune-mediated diseases, the female datasets were compared with similar public available male datasets. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

24 Samples

Download data: TXT

(Submitter supplied) DNA methylation has an impact on regulation of gene expression, however the relation between the two is complex. By performing an integrative analysis of the methylome and transcriptome of the four main circulating immune cell-subsets from healthy females, namely B cells, monocytes, CD4 and CD8 T cells, the relation between the two was characterized. In addition, in light of the known sex bias in the prevalence of several immune-mediated diseases, the female datasets were compared with similar public available male datasets. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

24 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

Platform:

GPL11154

40 Samples

Download data: TXT