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Series GSE223748 Query DataSets for GSE223748
Status Public on Aug 05, 2023
Title Mammalian Methylation Consortium
Platform organisms Homo sapiens; Mus musculus; Rattus norvegicus
Sample organisms Ornithorhynchus anatinus; Tachyglossus aculeatus; Didelphis virginiana; Didelphis marsupialis; Sarcophilus harrisii; Notamacropus agilis; Notamacropus eugenii; Macropus fuliginosus; Macropus giganteus; Osphranter robustus; Osphranter rufus; Tamandua mexicana; Bradypus variegatus; Choloepus hoffmanni; Dasypus novemcinctus; Erinaceus europaeus; Atelerix albiventris; Echinops telfairi; Suncus murinus; Sorex hoyi; Blarina brevicauda; Amblysomus hottentotus; Pteropus poliocephalus; Pteropus hypomelanus; Rousettus aegyptiacus; Artibeus jamaicensis; Phyllostomus hastatus; Desmodus rotundus; Tadarida brasiliensis; Antrozous pallidus; Lemur catta; Varecia variegata; Cheirogaleus medius; Otolemur crassicaudatus; Loris tardigradus; Nycticebus coucang; Perodicticus potto; Callithrix jacchus; Macaca mulatta; Papio hamadryas; Gorilla gorilla; Pan troglodytes; Pongo pygmaeus; Homo sapiens; Canis latrans; Canis lupus familiaris; Lycaon pictus; Vulpes vulpes; Ursus americanus; Martes americana; Mustela putorius furo; Crocuta crocuta; Felis catus; Panthera leo; Panthera tigris; Puma concolor; Zalophus californianus; Odobenus rosmarus divergens; Phoca vitulina; Delphinus delphis; Orcinus orca; Tursiops truncatus; Phocoena phocoena; Delphinapterus leucas; Physeter catodon; Balaenoptera borealis; Balaenoptera musculus; Megaptera novaeangliae; Trichechus manatus; Elephas maximus; Loxodonta africana; Equus grevyi; Equus caballus; Diceros bicornis; Rhinoceros unicornis; Procavia capensis; Orycteropus afer; Sus scrofa; Sus scrofa domesticus; Capreolus capreolus; Cervus elaphus; Odocoileus virginianus; Muntiacus vaginalis; Giraffa camelopardalis; Aepyceros melampus; Bos taurus; Capra hircus; Ovis aries; Tragelaphus oryx; Tragelaphus strepsiceros; Tragelaphus imberbis; Ochotona princeps; Oryctolagus cuniculus; Sylvilagus floridanus; Marmota monax; Tamiasciurus hudsonicus; Cricetulus griseus; Cricetulus longicaudatus; Mesocricetus auratus; Peromyscus leucopus; Peromyscus maniculatus; Meriones unguiculatus; Microtus pennsylvanicus; Ondatra zibethicus; Acomys cahirinus; Cricetomys gambianus; Mus musculus; Mus minutoides; Rattus norvegicus; Rattus rattus; Apodemus sylvaticus; Hystrix cristata; Cavia porcellus; Galea musteloides; Hydrochoerus hydrochaeris; Myocastor coypus; Bathyergus janetta; Bathyergus suillus; Cryptomys hottentotus; Georychus capensis; Heterocephalus glaber; Eulemur coronatus; Eulemur fulvus; Hapalemur griseus; Monodelphis domestica; Nanger granti; Balaena mysticetus; Lagenorhynchus albirostris; Molossus molossus; Nycticeius humeralis; Choloepus didactylus; Elephantulus edwardii; Eptesicus fuscus; Chaetophractus villosus; Macroscelides proboscideus; Vombatus ursinus; Vicugna pacos; Sylvilagus audubonii; Propithecus tattersalli; Eulemur macaco; Microcebus murinus; Galago moholi; Nannospalax ehrenbergi; Sciurus carolinensis; Daubentonia madagascariensis; Acinonyx jubatus; Dromiciops gliroides; Eulemur mongoz; Eulemur rubriventer; Chinchilla lanigera; Erethizon dorsatum; Sciurus niger; Oreamnos americanus; Enhydra lutris; Eumetopias jubatus; Sorex cinereus; Suricata suricatta; Hippotragus equinus; Hippotragus niger; Tupaia belangeri; Cavia aperea; Caenolestes fuliginosus; Globicephala macrorhynchus; Phascolarctos cinereus; Apodemus agrarius; Phoca groenlandica; Carollia perspicillata; Ochotona rufescens; Peromyscus eremicus; Peromyscus polionotus; Peromyscus californicus; Ictidomys tridecemlineatus; Tamias striatus; Glaucomys sabrinus; Steno bredanensis; Sorex palustris; Eulemur fulvus collaris; Phodopus campbelli; Lepus americanus; Lepus californicus; Mesoplodon bidens; Tamandua tetradactyla; Cabassous unicinctus; Hylomys suillus; Sylvilagus nuttallii; Urocitellus columbianus; Talpa occidentalis; Myotis myotis; Nyctalus noctula; Jaculus jaculus; Castor canadensis; Aplodontia rufa; Callithrix geoffroyi; Trachypithecus francoisi; Mustela frenata; Cynopterus brachyotis; Myotis lucifugus; Pipistrellus pipistrellus; Rhinolophus ferrumequinum; Saccopteryx bilineata; Addax nasomaculatus; Antidorcas marsupialis; Kobus megaceros; Chlorocebus sabaeus; Arvicanthis niloticus; Lynx rufus; Plecotus auritus; Ctenomys lewisi; Ctenomys opimus; Ctenomys steinbachi; Sorex minutissimus; Sorex caecutiens; Sorex isodon; Neomys fodiens; Sorex tundrensis; Sorex roboratus; Sorex vagrans; Sorex trowbridgii; Tamias amoenus; Tragelaphus angasii; Nanger dama; Chrysocyon brachyurus; Tragelaphus eurycerus; Tragelaphus spekii; Gazella leptoceros; Nanger soemmerringii; Eudorcas thomsonii; Litocranius walleri; Tupaia tana; Scalopus aquaticus; Equus asinus somalicus; Ceratotherium simum simum; Dipus sagitta; Callospermophilus lateralis; Eidolon helvum; Pteropus rodricensis; Microtus ochrogaster; Tursiops aduncus; Propithecus diadema; Cyclopes didactylus; Okapia johnstoni; Eulemur flavifrons; Equus quagga; Phyllostomus discolor; Lagenorhynchus obliquidens; Mustela altaica; Marmota flaviventris; Parascalops breweri; Tenrec ecaudatus; Callospermophilus saturatus; Alexandromys fortis; Xanthonycticebus pygmaeus; Connochaetes taurinus albojubatus; Napaeozapus insignis; Eozapus setchuanus; Cephalorhynchus commersonii; Neotoma cinerea; Apodemus peninsulae; Cuniculus paca; Myotis brandtii; Myotis nattereri; Phodopus roborovskii; Microtus richardsoni; Elephantulus myurus; Rhabdomys pumilio; Eulemur sanfordi; Tamias townsendii; Rhinopoma hardwickii; Ochotona alpina; Ochotona dauurica; Ochotona hyperborea; Ochotona pallasi; Pteropus vampyrus; Apodemus uralensis; Cavia tschudii; Pteropus giganteus; Condylura cristata; Tamiasciurus douglasii; Myotis thysanodes; Myotis yumanensis; Pteropus pumilus; Neophoca cinerea; Zapus princeps; Scapanus orarius; Neurotrichus gibbsii; Tolypeutes matacus; Rhombomys opimus; Hemiechinus auritus; Myotis vivesi; Orientallactaga sibirica; Mops pumilus; Tupaia longipes; Rhynchonycteris naso; Rhinolophus alcyone; Myotis evotis; Paraechinus aethiopicus; Microtus guentheri; Gerbillus nanus; Meriones rex; Meriones libycus; Smutsia temminckii; Hemicentetes semispinosus; Setifer setosus; Tupaia gracilis; Ellobius talpinus; Cricetulus barabensis; Microgale cowani; Mirza zaza; Alticola semicanus; Dendrohyrax arboreus; Suncus varilla; Sylvilagus bachmani; Propithecus coquereli; Lasiopodomys mandarinus; Alticola barakshin; Lasiopodomys brandtii; Aonyx cinereus; Neogale vison; Crocidura cyanea; Hipposideros ruber; Alexandromys maximowiczii; Micaelamys namaquensis; Clethrionomys gapperi; Galeopterus variegatus; Sylvilagus brasiliensis; Varecia rubra; Asellia tridens; Galea musteloides leucoblephara; Leptonycteris yerbabuenae; Alexandromys mongolicus; Eulemur rufus; Fukomys damarensis; Nannospalax galili; Cephalorhynchus hectori hectori; Eulemur albifrons; Cephalorhynchus hectori maui; Paraechinus hypomelas; Gerbillus cheesmani; Microgale thomasi; Cervus canadensis; Microgale drouhardi; Notamacropus rufogriseus; Alexandromys oeconomus; Nesogale talazaci; Myodes rufocanus; Nothocricetulus migratorius; Stenocranius gregalis
Experiment type Methylation profiling by array
Summary 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). Most of the CpGs are located in highly conserved stretches of DNA but not all CpGs apply to all species as detailed in the description of the platform, GPL28271 and on https://github.com/shorvath/MammalianMethylationConsortium/.
 
Overall design Cytosine methylation data from the following species and tissues. Subsets of these data are available in other accession numbers: GSE174758, GSE184211, GSE184213, GSE184215, GSE184216, GSE184218, GSE184220, GSE184221, GSE184224, GSE190660, GSE190661, GSE190662, GSE190663, GSE190664, GSE174544, GSE190665, GSE174767, GSE184222, GSE184223, GSE174777, GSE174778, GSE173330, GSE164127, GSE147002,GSE147003, GSE147004.
Web link https://www.science.org/doi/10.1126/science.abq5693
 
Contributor(s) Horvath S
Citation(s) 37561875, 37563227, 38848365
Submission date Jan 25, 2023
Last update date Jun 26, 2024
Contact name Steve Horvath
E-mail(s) shorvath@altoslabs.com
Organization name University of California, Los Angeles
Department Human Genetics
Lab Horvath
Street address 695 Charles E. Young Drive South, Box 708822
City Los Angeles
State/province CA
ZIP/Postal code 90095-7088
Country USA
 
Platforms (1)
GPL28271 Illumina HorvathMammalianMethylChip40 BeadChip
Samples (15043)
GSM6979529 genomic DNA from Mouse Cerebellum 202897220093_R01C01
GSM6979530 genomic DNA from Mouse Cerebellum 202897220093_R02C01
GSM6979531 genomic DNA from Mouse Cerebellum 202897220093_R03C01
Relations
BioProject PRJNA928364

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE223748_Explanation_of_characteristic_variables.docx.gz 15.4 Kb (ftp)(http) DOCX
GSE223748_RAW.tar 11.0 Gb (http)(custom) TAR (of IDAT)
GSE223748_README.GEO.docx 16.8 Kb (ftp)(http) DOCX
GSE223748_datBetaNormalized.csv.gz 4.2 Gb (ftp)(http) CSV
Processed data are available on Series record
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