GEO DataSets

(Submitter supplied) Cytosine methylation data generated on mammalian methylation platform

Organism:

Zalophus californianus; Phoca vitulina; Rattus norvegicus; Eumetopias jubatus; Neophoca cinerea; Homo sapiens; Mus musculus; Odobenus rosmarus divergens; Phoca groenlandica

Type:

Methylation profiling by array

Platform:

GPL28271

171 Samples

Download data: CSV, IDAT

(Submitter supplied) An Infinium microarray platform (GPL28271, HorvathMammalMethylChip40) was used to generate DNA methylation data from several tissues (skin, blood) in toothed whales and dolphins. Tissues: skin and blood.

Organism:

Delphinapterus leucas; Mus musculus; Rattus norvegicus; Lagenorhynchus obliquidens; Homo sapiens; Phocoena phocoena; Orcinus orca; Tursiops truncatus; Globicephala macrorhynchus; Steno bredanensis; Delphinus delphis; Cephalorhynchus commersonii

Type:

Methylation profiling by genome tiling array

Platform:

GPL28271

545 Samples

Download data: IDAT, TXT

(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

(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

Platforms:

GPL21103 GPL17021

549 Samples

Download data: TXT

(Submitter supplied) An Infinium microarray platform (GPL28271, HorvathMammalMethylChip40) was used to generate DNA methylation data from skin samples of beluga whales, Maui's dolphin, and humpback whale. Tissue: Skin

Organism:

Homo sapiens; Physeter catodon; Delphinapterus leucas; Mus musculus; Rattus norvegicus; Cephalorhynchus hectori maui; Balaenoptera musculus; Megaptera novaeangliae

Type:

Methylation profiling by genome tiling array

Platform:

GPL28271

143 Samples

Download data: IDAT

(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:

Mus musculus; Macaca mulatta; Homo sapiens; Rattus norvegicus

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:

Rattus norvegicus; Homo sapiens; Chlorocebus sabaeus; Mus musculus

Type:

Methylation profiling by array

Platform:

GPL28271

240 Samples

Download data: CSV, DOCX, IDAT

(Submitter supplied) DNA methylation data from common marmosets (Callithrix jacchus) profiled on the mammalian methylation array (HorvathMammalMethylChip40) which focuses on highly conserved CpGs across mammalian species. Rapamycin study in a subset of animals.

Organism:

Homo sapiens; Mus musculus; Callithrix jacchus; Rattus norvegicus

Type:

Methylation profiling by array

Platform:

GPL28271

96 Samples

Download data: CSV, DOCX, IDAT

(Submitter supplied) An Infinium microarray platform (GPL28271, HorvathMammalMethylChip40) was used to generate DNA methylation data from many tissues of plains zebras (Equus quagga). Both whole blood (96) and remote biopsy (24) samples were obtained from a captive population of zebras maintained in a semi-wild state. After eliminating samples with low confidence for individual identity and age, we retained 76 blood samples and 20 biopsy samples, totaling 96 zebra samples.

Organism:

Rattus norvegicus; Homo sapiens; Mus musculus; Equus quagga burchellii

Type:

Methylation profiling by array

Platform:

GPL28271

118 Samples

Download data: CSV, DOCX, IDAT

(Submitter supplied) An Infinium microarray platform (GPL28271, HorvathMammalMethylChip40) was used to generate DNA methylation data from blood samples in two equid species: Somali wild ass and Grevy's zebra. n=12 blood samples

Organism:

Equus grevyi; Equus asinus somalicus; Mus musculus; Rattus norvegicus; Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL28271

12 Samples

Download data: CSV, DOCX, IDAT

(Submitter supplied) An Infinium microarray platform (GPL28271, HorvathMammalMethylChip40) was used to generate DNA methylation data from many tissues from horses We generated DNA methylation data from n=333 horse tissue samples representing tissues. Blood samples were collected via venipuncture into EDTA tubes from across 24 different horse breeds (buffy coat). The other tissues were collected at necropsy. The tissue atlas was generated from two Thoroughbred mares as part of the FAANG initiative 37, with the following tissues profiled: adipose (gluteal), adrenal cortex, blood (PBMCs; only n=1 mare), cartilage (only n=1 mare), cecum, cerebellum (2 samples each from lateral hemisphere and vermis), frontal cortex, duodenum, fibroblast, heart (2 samples each from the right atrium, left atrium, right ventricle, left ventricle), hypothalamus, ileum, jejunum, keratinocyte, kidney (kidney cortex and medulla), lamina, larynx (i.e. more...

Organism:

Homo sapiens; Equus caballus; Rattus norvegicus; Mus musculus

Type:

Methylation profiling by array

Platform:

GPL28271

333 Samples

Download data: IDAT, TXT

(Submitter supplied) The naked mole-rat, Heterocephalus glaber (NMR), the longest-lived rodent with a maximum possible lifespan exceeding 33 years, is emerging as an important non-model organism for the study of longevity and healthspan. As such it is of significance and interest in the study of biomarkers for ageing in mammals. Recent breakthroughs in this field have indicated that ‘epigenetic clocks’ based on the temporal accumulation of DNA methylation at specific genomic sites can enable accurate age estimates for tissues across the lifespan of an individual. more...

Organism:

Heterocephalus glaber

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL27526

39 Samples

Download data: CSV

(Submitter supplied) We used blood samples from Macaque to determine rate of change of methylation with respect to age.

Organism:

Homo sapiens; Macaca mulatta

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

6 Samples

Download data

(Submitter supplied) We used liver samples from TC1 Mice to determine rate of change of methylation with respect to age.

Organism:

Homo sapiens; Mus musculus

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

6 Samples

Download data: TXT

(Submitter supplied) We used liver samples from Naked Mole Rat to determine rate of change of methylation with respect to age.

Organism:

Heterocephalus glaber

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL24046

24 Samples

Download data: TXT

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

Organism:

Mus musculus; Heterocephalus glaber; Homo sapiens; Canis lupus familiaris; Macaca mulatta

Type:

Methylation profiling by high throughput sequencing; Methylation profiling by genome tiling array

Platforms:

GPL24046 GPL13534 GPL22370

84 Samples

Download data: TXT

(Submitter supplied) We used buccal samples from two different dog breeds with well established differences in average lifespan to perform genome-scale identification of ageing-associated differentially methylated positions (aDMPs) in a total of 48 different dogs. A significant proportion of aDMPs that gained methylation with age replicated in an independent cohort. Furthermore, we also show that human aDMPs show similar ageing-associated dynamics at the homologous genomic regions in the dog. more...

Organism:

Canis lupus familiaris

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL22370

48 Samples

Download data: TXT

(Submitter supplied) An Infinium microarray platform (GPL28271, Horvath MammalMethylChip40) was used to generate DNA methylation data from skin samples of Hector's and Māui dolphins.

Organism:

Mus musculus; Homo sapiens; Rattus norvegicus; Cephalorhynchus hectori hectori; Cephalorhynchus hectori maui

Type:

Methylation profiling by genome tiling array

Platform:

GPL28271

141 Samples

Download data: 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:

GPL21145 GPL13534

334 Samples

Download data: IDAT