GEO DataSets

(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) 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:

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; Homo sapiens; Macaca mulatta

Type:

Expression profiling by array

Platforms:

GPL570 GPL3535

48 Samples

Download data: CEL, TXT

(Submitter supplied) DNA methylation data from rhesus macaque (Macaca mulatta) profiled on the mammalian methylation array (HorvathMammalMethylChip40) which focuses on highly conserved CpGs across mammalian species. We profiled n = 283 tissue samples (blood, skin, adipose, kidney, liver, lung, muscle, and cerebral cortex)

Organism:

Rattus norvegicus; Mus musculus; Macaca mulatta; Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL28271

283 Samples

Download data: CSV, DOCX, IDAT

(Submitter supplied) DNA methylation data from vervet cerebral cortex, blood, and liver using highly conserved mammalian CpGs represented on the mammalian methylation array (HorvathMammalMethylChip40). We selected a total of 240 samples representing the entire vervet lifespan, from neonatal to senile stages: 144 samples from the peripheral blood, 48 samples from the liver, and 48 samples from the cortical brain area BA10.

Organism:

Homo sapiens; Chlorocebus sabaeus; Mus musculus; Rattus norvegicus

Type:

Methylation profiling by array

Platform:

GPL28271

240 Samples

Download data: CSV, DOCX, IDAT

(Submitter supplied) In this study, we have optimized and directly compared epigenetic age predictors based on pyrosequencing, ddPCR and BBA-seq of specific age-associated regions. Bisulfite barcoded amplicon sequencing (BBA-seq) was performed on 9 genomic region of 77 human blood DNA and 11 genomic regions of 95 buccal swab DNA to measure age-associated regions for epigenetic age prediction. Furthermore, our data indicate that the correlation of age-associated DNAm with chronological age peaks close to CTCF binding sites. more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL15520

172 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) DNA methylation data from several primate species profiled on the mammalian methylation array (HorvathMammalMethylChip40) which focuses on highly conserved CpGs across mammalian species. We selected a total of 91 samples from animals representing 26 strepsirrhine species, in most cases, the entire lifespan, from immature (infant or juvenile) to senile stages: 68 samples from peripheral blood, 23 samples from skin Blood and skin samples from many different primates. more...

Organism:

Lemur catta; Cheirogaleus medius; Homo sapiens; Eulemur fulvus; Hapalemur griseus; Eulemur macaco; Propithecus coquereli; Otolemur crassicaudatus; Eulemur coronatus; Eulemur rubriventer; Eulemur fulvus collaris; Mirza zaza; Eulemur albifrons; Loris tardigradus; Nycticebus coucang; Mus musculus; Rattus norvegicus; Propithecus tattersalli; Galago moholi; Eulemur mongoz; Propithecus diadema; Eulemur flavifrons; Eulemur sanfordi; Perodicticus potto; Microcebus murinus; Daubentonia madagascariensis; Xanthonycticebus pygmaeus; Varecia rubra; Eulemur rufus

Type:

Methylation profiling by array

Platform:

GPL28271

91 Samples

Download data: CSV, DOCX, IDAT

(Submitter supplied) DNA methylation data from Papio hamadryas (baboons) profiled on the mammalian methylation array (HorvathMammalMethylChip40) which focuses on highly conserved CpGs across mammalian species. Seven tissue types (fetal cerebral cortex, adult cerebral cortex, cerebellum, adipose, heart, liver, and skeletal muscle) with ages ranging from late fetal life to 22.8 years of age.

Organism:

Mus musculus; Rattus norvegicus; Homo sapiens; Papio hamadryas

Type:

Methylation profiling by array

Platform:

GPL28271

325 Samples

Download data: CSV, DOCX, IDAT

(Submitter supplied) An Infinium microarray platform (GPL28271, HorvathMammalMethylChip40) was used to generate DNA methylation data from human cell types. n=17 human DNA samples from endothelial cells (n=13), embryonic stem cells (n=2) and skin (n=2).

Organism:

Homo sapiens; Mus musculus; Rattus norvegicus

Type:

Methylation profiling by array

Platform:

GPL28271

17 Samples

Download data: CSV, DOCX, IDAT

(Submitter supplied) An Infinium microarray platform (GPL28271, HorvathMammalMethylChip40) was used to generate DNA methylation data from human tissue samples. n=144 EDTA blood samples and n=240 blood samples

Organism:

Homo sapiens; Mus musculus; Rattus norvegicus

Type:

Methylation profiling by array

Platform:

GPL28271

384 Samples

Download data: CSV, DOCX, IDAT

(Submitter supplied) An Infinium microarray platform (GPL28271, HorvathMammalMethylChip40) was used to generate DNA methylation data from human blood samples. n=92 brain samples (n=46 samples from cerebellum, n=46 from cerebral cortex).

Organism:

Rattus norvegicus; Homo sapiens; Mus musculus

Type:

Methylation profiling by array

Platform:

GPL28271

92 Samples

Download data: CSV, DOCX, IDAT

(Submitter supplied) An Infinium microarray platform (GPL28271, HorvathMammalMethylChip40) was used to generate DNA methylation data from human tissue samples. n=96 tissues. Skin (n=72), keratinocyte (n=20), fibroblast (1), epidermis (2), dermis (1)

Organism:

Rattus norvegicus; Mus musculus; Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL28271

96 Samples

Download data: CSV, DOCX, IDAT

(Submitter supplied) Genome wide DNA methylation profiling of normal colon samples. The Illumina Infinium HumanMethylation450 and EPIC Beadchip arrays were used to obtain DNA methylation profiles across approximately 450,000 and 850,000 CpGs. Samples were from nomal colons of 334 subjects with low, medium or high CRC risk according to their personal adenoma or cancer history.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platforms:

GPL13534 GPL21145

334 Samples

Download data: IDAT

(Submitter supplied) This dataset contains 78 vastus lateralis muscle samples from healthy men who underwent 1) an acute bout of HIIT and 2) four weeks of HIIT.

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL21145

78 Samples

Download data: IDAT, TXT

(Submitter supplied) An Infinium microarray platform (GPL28271, HorvathMammalMethylChip40) was used to generate DNA methylation data from blood samples of roe deer n=94 blood samples

Organism:

Capreolus capreolus; Rattus norvegicus; Homo sapiens; Mus musculus

Type:

Methylation profiling by array

Platform:

GPL28271

94 Samples

Download data: CSV, DOCX, IDAT

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

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing; Third-party reanalysis

Platforms:

GPL21103 GPL17021

549 Samples

Download data: CSV, TXT

(Submitter supplied) Human DNA-methylation data have been used to develop highly accurate biomarkers of aging ("epigenetic clocks"). Recent studies demonstrate that similar epigenetic clocks for mice (Mus Musculus) can be slowed by gold standard anti-aging interventions such as calorie restriction and growth hormone receptor knock-outs. Using DNA methylation data from previous publications with data collected in house for a total 1189 samples spanning 193,651 CpG sites, we developed 4 novel epigenetic clocks by choosing different regression models (elastic net- versus ridge regression) and by considering different sets of CpGs (all CpGs vs highly conserved CpGs). more...

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing; Third-party reanalysis

Download data: TXT