GEO DataSets

(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) 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:

Mus musculus; Homo sapiens

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) The naked mole-rat (NMR) is an exceptionally long-lived rodent that does not show increased mortality with age, uniquely defining NMR as a demographically non-aging mammal. Here, we performed bisulfite sequencing on over one hundred NMR blood samples differing in age, assessing more than 3 million common CpG sites. We observed an information loss of the NMR methylome during aging suggesting that NMR ages. more...

Organism:

Heterocephalus glaber

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL21195

107 Samples

Download data: COV

(Submitter supplied) Background: DNA-methylation changes at a discrete set of sites in the human genome are predictive of chronological and biological age. However, it is not known whether these changes are causative or a consequence of an underlying ageing programme. It has also not been shown whether this ‘epigenetic clock’ is unique to humans or conserved in other animals such as the experimentally tractable mouse. Results: We have generated a comprehensive set of whole genome base-resolution methylation maps from multiple mouse tissues spanning a wide range of ages. more...

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL13112

62 Samples

Download data: TXT

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

Organism:

Mus musculus; Rattus norvegicus; Homo sapiens; Orcinus orca

Type:

Methylation profiling by array

Platform:

GPL28271

140 Samples

Download data: CSV, IDAT

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

Organism:

Homo sapiens; Mus musculus; Rattus norvegicus; Balaena mysticetus

Type:

Methylation profiling by array

Platform:

GPL28271

105 Samples

Download data: CSV, 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:

GPL17021 GPL21103

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:

GPL17021 GPL21103

549 Samples

Download data: TXT

(Submitter supplied) The goal was to find genes which are differentially expressed between the naked mole-rat (Heterocephalus glaber) and the wild-type mice liver tissue. The genes which are most differentially expressed may provide a clue for the remarkable differences between naked mole-rat and mouse in terms of longevity, cancer resistance and adaptation to subterranean environments.

Organism:

Heterocephalus glaber; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL9185 GPL13940

2 Samples

Download data: TXT

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

Organism:

Mus musculus; Macaca mulatta; Homo sapiens; Rattus

Type:

Methylation profiling by genome tiling array

Platform:

GPL32543

96 Samples

Download data: IDAT

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

Organism:

Macaca mulatta; Homo sapiens; Rattus; Mus musculus

Type:

Methylation profiling by genome tiling array

Platform:

GPL32543

95 Samples

Download data: IDAT

(Submitter supplied) The Mammalian Methylation Consortium aimed to characterize the relationship between cytosine methylation levels and a) species characteristics such as maximum lifespan and b) individual sample characteristics such as age, sex, tissue type. Both supervised machine learning approaches and unsupervised machine learning approaches were applied to the data as described in the citations. To facilitate comparative analyses across species, the mammalian methylation consortium applied a single measurement platform (the mammalian methylation array, GPL28271) to n=15216 DNA samples derived from 70 tissue types of 348 different mammalian species (331 eutherian-, 15 marsupial-, and 2 monotreme species). more...

Organism:

Ornithorhynchus anatinus; Notamacropus eugenii; Osphranter rufus; Suncus murinus; Tadarida brasiliensis; Antrozous pallidus; Nycticebus coucang; Perodicticus potto; Macaca mulatta; Canis latrans; Mustela putorius furo; Panthera leo; Panthera tigris; Puma concolor; Delphinus delphis; Megaptera novaeangliae; Equus caballus; Orycteropus afer; Tragelaphus imberbis; Tamiasciurus hudsonicus; Cricetulus longicaudatus; Mesocricetus auratus; Meriones unguiculatus; Cricetomys gambianus; Galea musteloides; Hydrochoerus hydrochaeris; Bathyergus suillus; Lagenorhynchus albirostris; Macroscelides proboscideus; Sciurus carolinensis; Daubentonia madagascariensis; Eulemur rubriventer; Oreamnos americanus; Enhydra lutris; Hippotragus equinus; Hippotragus niger; Globicephala macrorhynchus; Apodemus agrarius; Carollia perspicillata; Peromyscus californicus; Tamias striatus; Steno bredanensis; Phodopus campbelli; Hylomys suillus; Urocitellus columbianus; Jaculus jaculus; Callithrix geoffroyi; Mustela frenata; Ctenomys lewisi; Sorex roboratus; Tamias amoenus; Tragelaphus angasii; Chrysocyon brachyurus; Nanger soemmerringii; Eudorcas thomsonii; Dipus sagitta; Tursiops aduncus; Tenrec ecaudatus; Neotoma cinerea; Microtus richardsoni; Pteropus giganteus; Pteropus pumilus; Mops pumilus; Meriones libycus; Setifer setosus; Ellobius talpinus; Cricetulus barabensis; Suncus varilla; Lasiopodomys mandarinus; Aonyx cinereus; Varecia rubra; Leptonycteris yerbabuenae; Eulemur rufus; Fukomys damarensis; Eulemur albifrons; Gerbillus cheesmani; Microgale drouhardi; Notamacropus rufogriseus; Nesogale talazaci; Didelphis virginiana; Didelphis marsupialis; Notamacropus agilis; Macropus fuliginosus; Choloepus hoffmanni; Amblysomus hottentotus; Artibeus jamaicensis; Varecia variegata; Cheirogaleus medius; Gorilla gorilla; Pongo pygmaeus; Homo sapiens; Crocuta crocuta; Phoca vitulina; Phocoena phocoena; Delphinapterus leucas; Physeter catodon; Diceros bicornis; Odocoileus virginianus; Muntiacus vaginalis; Bos taurus; Tragelaphus oryx; Sylvilagus floridanus; Peromyscus maniculatus; Microtus pennsylvanicus; Mus musculus; Cryptomys hottentotus; Hapalemur griseus; Nanger granti; Balaena mysticetus; Molossus molossus; Nycticeius humeralis; Elephantulus edwardii; Sylvilagus audubonii; Propithecus tattersalli; Nannospalax ehrenbergi; Sciurus niger; Sorex cinereus; Tupaia belangeri; Cavia aperea; Phascolarctos cinereus; Ochotona rufescens; Sorex palustris; Cabassous unicinctus; Myotis myotis; Aplodontia rufa; Pipistrellus pipistrellus; Saccopteryx bilineata; Addax nasomaculatus; Antidorcas marsupialis; Kobus megaceros; Chlorocebus sabaeus; Ctenomys opimus; Neomys fodiens; Sorex vagrans; Eidolon helvum; Pteropus rodricensis; Okapia johnstoni; Phyllostomus discolor; Lagenorhynchus obliquidens; Osphranter robustus; Bradypus variegatus; Echinops telfairi; Blarina brevicauda; Desmodus rotundus; Pan troglodytes; Lycaon pictus; Vulpes vulpes; Felis catus; Zalophus californianus; Orcinus orca; Tursiops truncatus; Balaenoptera borealis; Callospermophilus saturatus; Alexandromys fortis; Xanthonycticebus pygmaeus; Cephalorhynchus commersonii; Cuniculus paca; Myotis brandtii; Myotis nattereri; Elephantulus myurus; Rhabdomys pumilio; Pteropus vampyrus; Apodemus uralensis; Condylura cristata; Tamiasciurus douglasii; Neurotrichus gibbsii; Rhombomys opimus; Rhinolophus alcyone; Myotis evotis; Meriones rex; Hemicentetes semispinosus; Microgale cowani; Dendrohyrax arboreus; Propithecus coquereli; Hipposideros ruber; Alexandromys maximowiczii; Galea musteloides leucoblephara; Alexandromys mongolicus; Nannospalax galili; Lasiopodomys gregalis; Balaenoptera musculus; Trichechus manatus; Equus grevyi; Sus scrofa; Giraffa camelopardalis; Capra hircus; Ovis aries; Tragelaphus strepsiceros; Oryctolagus cuniculus; Marmota monax; Cricetulus griseus; Ondatra zibethicus; Acomys cahirinus; Apodemus sylvaticus; Hystrix cristata; Bathyergus janetta; Georychus capensis; Eulemur coronatus; Eulemur fulvus; Vicugna pacos; Eulemur macaco; Microcebus murinus; Chinchilla lanigera; Erethizon dorsatum; Eumetopias jubatus; Caenolestes fuliginosus; Peromyscus eremicus; Peromyscus polionotus; Eulemur fulvus collaris; Lepus californicus; Tamandua tetradactyla; Talpa occidentalis; Myotis lucifugus; Rhinolophus ferrumequinum; Arvicanthis niloticus; Sorex caecutiens; Sorex isodon; Litocranius walleri; Scalopus aquaticus; Equus asinus somalicus; Ceratotherium simum simum; Callospermophilus lateralis; Mustela altaica; Napaeozapus insignis; Apodemus peninsulae; Ochotona alpina; Scapanus orarius; Hemiechinus auritus; Orientallactaga sibirica; Rhynchonycteris naso; Gerbillus nanus; Tupaia gracilis; Sylvilagus bachmani; Alticola barakshin; Asellia tridens; Myodes rufocanus; Nothocricetulus migratorius; Tachyglossus aculeatus; Sarcophilus harrisii; Macropus giganteus; Tamandua mexicana; Dasypus novemcinctus; Erinaceus europaeus; Atelerix albiventris; Sorex hoyi; Pteropus poliocephalus; Pteropus hypomelanus; Rousettus aegyptiacus; Phyllostomus hastatus; Lemur catta; Otolemur crassicaudatus; Loris tardigradus; Callithrix jacchus; Papio hamadryas; Canis lupus familiaris; Ursus americanus; Martes americana; Odobenus rosmarus divergens; Elephas maximus; Loxodonta africana; Rhinoceros unicornis; Procavia capensis; Sus scrofa domesticus; Capreolus capreolus; Cervus elaphus; Aepyceros melampus; Ochotona princeps; Peromyscus leucopus; Mus minutoides; Rattus norvegicus; Rattus rattus; Cavia porcellus; Myocastor coypus; Heterocephalus glaber; Monodelphis domestica; Choloepus didactylus; Eptesicus fuscus; Chaetophractus villosus; Vombatus ursinus; Galago moholi; Acinonyx jubatus; Dromiciops gliroides; Eulemur mongoz; Suricata suricatta; Phoca groenlandica; Ictidomys tridecemlineatus; Glaucomys sabrinus; Lepus americanus; Mesoplodon bidens; Sylvilagus nuttallii; Nyctalus noctula; Castor canadensis; Trachypithecus francoisi; Cynopterus brachyotis; Lynx rufus; Plecotus auritus; Ctenomys steinbachi; Sorex minutissimus; Sorex tundrensis; Sorex trowbridgii; Nanger dama; Tragelaphus eurycerus; Tragelaphus spekii; Gazella leptoceros; Tupaia tana; Microtus ochrogaster; Propithecus diadema; Cyclopes didactylus; Eulemur flavifrons; Equus quagga; Marmota flaviventris; Parascalops breweri; Connochaetes taurinus albojubatus; Eozapus setchuanus; Phodopus roborovskii; Eulemur sanfordi; Tamias townsendii; Rhinopoma hardwickii; Ochotona dauurica; Ochotona hyperborea; Ochotona pallasi; Cavia tschudii; Myotis thysanodes; Myotis yumanensis; Neophoca cinerea; Zapus princeps; Tolypeutes matacus; Myotis vivesi; Tupaia longipes; Paraechinus aethiopicus; Microtus guentheri; Smutsia temminckii; Mirza zaza; Alticola semicanus; Lasiopodomys brandtii; Neogale vison; Crocidura cyanea; Micaelamys namaquensis; Clethrionomys gapperi; Galeopterus variegatus; Sylvilagus brasiliensis; Cephalorhynchus hectori hectori; Cephalorhynchus hectori maui; Paraechinus hypomelas; Microgale thomasi; Cervus canadensis; Alexandromys oeconomus

Type:

Methylation profiling by array

Platform:

GPL28271

15043 Samples

Download data: CSV, DOCX, IDAT

(Submitter supplied) Partial reprogramming by expression of reprogramming factors (Oct4, Sox2, Klf4 and cMyc) for short periods of time restores a youthful epigenetic signature to aging cells and extends the lifespan of a premature aging mouse model. However, the effects of longer-term partial reprogramming in physiologically aging wild-type mice are unknown. Here, we have performed various long-term partial reprogramming regimens, including different onset timings, during physiological aging in different mouse strains. more...

Organism:

Rattus norvegicus; Homo sapiens; Mus musculus

Type:

Methylation profiling by array

Platform:

GPL28271

168 Samples

Download data: CSV, DOCX, 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:

Rattus norvegicus; Macaca mulatta; Homo sapiens; Mus musculus

Type:

Methylation profiling by array

Platform:

GPL28271

283 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:

Mus musculus; Callithrix jacchus; Rattus norvegicus; Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL28271

96 Samples

Download data: CSV, DOCX, IDAT