GEO DataSets

(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) 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:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL9448

3 Samples

Download data: PAIR

(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) 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) 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) To further our understanding of the role of DNA methylation in development, Methylated DNA Immunoprecipitation (MeDIP) was used in conjunction with a NimbleGen promoter plus CpG island array to identify Tissue and Developmental Stage specific Differentially Methylated DNA Regions (T-DMRs and DS-DMRs) on a genome-wide basis. Four tissues (brain, heart, liver, and testis) from C57BL/6J mice were analyzed at three developmental stages (15 day embryo, E15; new born, NB; 12 week adult, AD). more...

Organism:

Mus musculus

Type:

Methylation profiling by genome tiling array

Platform:

GPL7060

26 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) Compared with non-cancerous lung tissues, lung cancer in Xuanwei tissues expressed a total of 6,899 differentially methylated regions, including 5,788 hypermethylated regions and 1,111 hypomethylated regions. Many differentially methylated regions have been found in lung cancer in Xuanwei.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL16378

2 Samples

Download data: GFF, PAIR, XLS

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

Organism:

Homo sapiens; Mus musculus

Type:

Methylation profiling by genome tiling array

26 related Platforms

76 Samples

Download data: TXT

(Submitter supplied) Genomic imprinting describes the expression of a subset of mammalian genes from one parental chromosome. The parent-of-origin specific expression of imprinted genes relies on DNA methylation of CpG-dinucleotides at differentially methylated regions (DMRs) during gametogenesis. We identified the paternally methylated DMR at human chromosome 2 near the imprinted ZDBF2 gene using a methylated-DNA immunoprecipitation-on-chip (meDIP-on-chip) method applied to DNA from sperm.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL9641

1 Sample

Download data: TXT

(Submitter supplied) Genomic imprinting describes the expression of a subset of mammalian genes from one parental chromosome. The parent-of-origin specific expression of imprinted genes relies on DNA methylation of CpG-dinucleotides at differentially methylated regions (DMRs) during gametogenesis. We identified the paternally methylated DMRs at mouse chromosome 1 near the imprinted Zdbf2 gene using a methylated-DNA immunoprecipitation-on-chip (meDIP-on-chip) method applied to DNA from parthenogenetic (PG)- and androgenetic (AG)-derived cells and sperm. more...

Organism:

Mus musculus

Type:

Methylation profiling by genome tiling array

25 related Platforms

75 Samples

Download data: TXT

(Submitter supplied) Murine and non-human primates (e.g. rhesus monkeys) represent excellent model systems to study human health and disease. However, use of these model systems for genomic studies is limited, particularly with array-based tools, as most have only been developed to survey the human genome. Here we present the optimization of a widely used human DNA methylation array, designed to detect 5-methylcytosine (5-mC), and show that non-human data generated using the optimized array reproducibly distinguishes tissue types within and between chimpanzee, rhesus, and mouse, with correlations near the human DNA level (R2 > 0.99). more...

Organism:

Mus musculus; Macaca mulatta; Homo sapiens; Pan troglodytes

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

61 Samples

Download data: TXT

(Submitter supplied) We aim to discover differentially methylated regions (DMRs) in peripheral T cells involved in de novo cSCC development after kidney transplantation. This was a retrospective study on biobank patient material. We matched kidney transplant patients with (future) cSCC to those without cSCC and studied genome-wide DNA methylation (450k arrays) of T cells before transplantation.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

65 Samples

Download data: IDAT

(Submitter supplied) This study showed that MeDIP-seq could be used for methylation profiling in an efficient manner and identified a number of potential hub genes and pathways important in the ovarian cancer carcinogenesis that may deepen our understanding of the molecular mechanisms involved inthe development of ovarian cancer.

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL18573

8 Samples

Download data: XLSX

(Submitter supplied) This study sought to identify hub genes and prospective pathways that would help in comprehending the molecular mechanisms involved in the development of EOC. 

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

6 Samples

Download data: XLSX

(Submitter supplied) Background: C3H mice have been frequently used in cancer studies as animal models of spontaneous liver tumors and chemically induced hepatocellular carcinoma (HCC). Epigenetic modifications, including DNA methylation, are among pivotal control mechanisms of gene expression leading to carcinogenesis. Although information on somatic mutations in liver tumors of C3H mice is available, epigenetic aspects are yet to be clarified. more...

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL17021

6 Samples

Download data: XLSX