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Series GSE195869 Query DataSets for GSE195869
Status Public on Jun 18, 2022
Title Comparative analysis of genome-scale, base-resolution DNA methylation profiles across 580 animal species
Organisms Riftia pachyptila; Mya arenaria; Loligo vulgaris; Illex illecebrosus; Octopus vulgaris; Homarus americanus; Pisaster brevispinus; Lytechinus variegatus; Strongylocentrotus purpuratus; Strongylocentrotus droebachiensis; Holothuria; Ciona intestinalis; Branchiostoma floridae; Leucoraja erinaceus; Squalus acanthias; Mustelus canis; Galeocerdo cuvier; Negaprion brevirostris; Callorhinchus milii; Clupea harengus; Danio rerio; Cyprinus carpio; Esox lucius; Salmo salar; Salmo trutta; Salvelinus alpinus; Gadus morhua; Pollachius virens; Lophius piscatorius; Hemitripterus americanus; Cyclopterus lumpus; Zoarces americanus; Thunnus albacares; Xiphias gladius; Myzopsetta ferruginea; Ambystoma; Ambystoma mexicanum; Chelydra serpentina; Emydidae; Graptemys; Testudinidae; Iguanidae; Tiliqua rugosa; Heloderma; Varanus; Varanus exanthematicus; Gekkonidae; Boa constrictor; Natrix tessellata; Naja; Vipera ammodytes; Crotalus; Casuarius casuarius; Dromaius novaehollandiae; Rhea americana; Struthio camelus; Anas platyrhynchos; Dendrocygna viduata; Charadriidae; Ciconiidae; Ciconia ciconia; Columbidae; Columba livia; Falco peregrinus; Accipiter gentilis; Circus aeruginosus; Haliaeetus albicilla; Acryllium vulturinum; Gallus; Gallus gallus; Perdix perdix; Phasianus colchicus; Coturnix coturnix; Coturnix delegorguei; Serinus; Parus major; Sturnus vulgaris; Phalacrocorax carbo; Phoenicopteriformes; Ara; Ara ararauna; Aptenodytes patagonicus; Spheniscus humboldti; Sarcophilus; Macropodidae; Macropus; Petauridae; Dasypodidae; Erinaceidae; Scandentia; Tupaia; Pteropus; Lemur; Varecia; Callithrix jacchus; Saguinus; Leontocebus fuscicollis; Saguinus mystax; Saguinus oedipus; Saguinus imperator; Cercopithecus; Macaca; Macaca sylvanus; Papio; Papio hamadryas; Theropithecus gelada; Colobus polykomos; Pongo; Canis lupus; Canis lupus familiaris; Vulpes vulpes; Ursus; Ursus arctos; Ailurus fulgens; Nasua; Procyon lotor; Mustelidae; Lutra lutra; Martes foina; Meles meles; Mustela; Mustela putorius; Felis silvestris; Felis catus; Panthera leo; Panthera onca; Panthera pardus; Panthera tigris; Puma concolor; Phocidae; Equus; Equus zebra; Tapirus; Rhinocerotidae; Sus scrofa; Sus scrofa domesticus; Tayassuidae; Camelus dromedarius; Lama glama; Tragulus javanicus; Cervidae; Capreolus capreolus; Cervus elaphus; Cervus nippon; Rangifer tarandus; Muntiacus; Ammotragus; Bison bonasus; Bos; Boselaphus tragocamelus; Bubalus; Capra; Capra aegagrus; Connochaetes; Ovis aries; Kobus; Capricornis; Lepus europaeus; Oryctolagus cuniculus; Marmota; Spermophilus; Cricetinae; Cricetus; Acomys; Mus musculus; Rattus norvegicus; Rattus rattus; Apodemus sylvaticus; Hystricidae; Caviidae; Hydrochoerus hydrochaeris; Lagostomus maximus; Myocastor coypus; Heterocephalus; Saccoglossus kowalevskii; Amazona; Lynx lynx; Melopsittacus; Nymphicus hollandicus; Psittacus; Tamias; Tinca tinca; Macroscelidea; Macroscelides proboscideus; Dolichotis; Dolichotis patagonum; Castoridae; Magallana gigas; Molgula citrina; Styela montereyensis; Botryllus schlosseri; Incilius alvarius; Duttaphrynus melanostictus; Heleophrynidae; Chauna torquata; Ardea; Buteo; Buteo buteo; Rollulus; Balearica pavonina; Grus japonensis; Corvus; Corvus corone; Strigiformes; Bubo bubo; Carcharias taurus; Axis axis; Dama dama; Vicugna pacos; Vicugna; Yinpterochiroptera; Yangochiroptera; Leontopithecus; Capromyidae; Hippoglossoides elassodon; Trachemys scripta elegans; Vipera berus; Acinonyx; Colobus guereza; Scopus umbretta; Gypaetus; Pelecanus; Morone saxatilis; Hippoglossoides platessoides; Glyptocephalus cynoglossus; Capromys pilorides; Erethizon; Rupicapra rupicapra; Nyctereutes; Petaurus breviceps; Trachemys; Pythonidae; Stenotomus chrysops; Zosteropidae; Pelecanus crispus; Strix uralensis; Cucumaria frondosa; Suricata; Hemitragus; Hippotragus; Hippotragus equinus; Chloris chloris; Coccothraustes; Vidua paradisaea; Ostrea edulis; Lepas anatifera; Cebinae; Phascolarctos cinereus; Leiocephalus; Polychrus marmoratus; Cricetomyinae; Carollia perspicillata; Chamaeleonidae; Uromastyx; Lutjanus mahogoni; Cynictis; Glis glis; Cygnus melancoryphus; Circus cyaneus; Milvus milvus; Oplurus; Pithecia pithecia; Erythrura; Bothriechis schlegelii; Cynomys; Brachylophus; Patiria miniata; Phodopus campbelli; Neoniphon sammara; Psammomys obesus; Sylvia atricapilla; Passer domesticus; Jaculus; Geochelone; Cyclura; Sauromalus; Python molurus; Python regius; Eunectes; Pogona barbata; Acanthosaura; Shinisaurus crocodilurus; Aquila heliaca; Haliaeetus leucocephalus; Plegadis falcinellus; Eliomys quercinus; Apodemus flavicollis; Cariamidae; Eurypygidae; Jacanidae; Macaca silenus; Sciurus vulgaris; Lissemys punctata; Musophagidae; Centropomus robalito; Corvus corax; Garrulus glandarius; Cyclura cornuta; Leontopithecus chrysomelas; Coliiformes; Upupa epops; Ecsenius; Cornufer guentheri; Antidorcas; Antilope; Kobus leche; Agapornis; Agapornis canus; Agapornis lilianae; Agapornis personatus; Agapornis taranta; Loriculus galgulus; Mimus polyglottos; Leptailurus; Varanus gouldii; Lepus timidus; Scincidae; Astrochelys radiata; Tragelaphus angasii; Paralichthys dentatus; Nanger dama; Myoxocephalus octodecemspinosus; Canis aureus; Tragelaphus spekii; Tiliqua scincoides; Sebastes atrovirens; Sebastes caurinus; Sebastes constellatus; Sebastes hopkinsi; Sebastes miniatus; Sebastes mystinus; Sebastes ovalis; Sebastes paucispinis; Sebastolobus alascanus; Hypselecara coryphaenoides; Geoemyda spengleri; Paracanthurus hepatus; Corvus frugilegus; Ariopsis felis; Spatula querquedula; Abronia anzuetoi; Eudyptes chrysocome; Dascyllus aruanus; Pomacentrus coelestis; Coryphaenoides acrolepis; Equus asinus asinus; Terrapene; Testudo hermanni; Mullus surmuletus; Lampropeltis; Pomatomus saltator; Corucia zebrata; Elephas maximus indicus; Embiotoca jacksoni; Paracirrhites forsteri; Falco tinnunculus; Geronticus eremita; Picus viridis; Tetrao urogallus; Testudo kleinmanni; Hoplobatrachus tigerinus; Musophaga; Nothobranchius furzeri; Scyliorhinus retifer; Fromia; Fromia indica; Nardoa novaecaledoniae; Osteoglossum bicirrhosum; Chaetodon lineolatus; Chaetodon lunula; Asio otus; Strix aluco; Buteo lagopus; Ducula bicolor; Ptilinopus; Trioceros jacksonii; Batoidea; Rhinoptera bonasus; Loweina terminata; Athene noctua; Theloderma; Penaeus; Nectariniidae; Ploceus cucullatus; Caiman yacare; Cacatua alba; Probosciger aterrimus; Monacanthidae; Polypedates otilophus; Correlophus ciliatus; Paroedura picta; Halichoeres trimaculatus; Rhinogobiops nicholsii; Spinus spinus; Phyllopteryx taeniolatus; Rhacophorus reinwardtii; Otaria; Tringa totanus; Recurvirostra avosetta; Leucoraja ocellata; Pycnonotus barbatus; Chloropsis; Irena puella; Psarisomus dalhousiae; Cynoscion regalis; Acanthurus triostegus; Ctenochaetus striatus; Tockus deckeni; Bycanistes bucinator; Alectis ciliaris; Chamaeleo calyptratus; Elops affinis; Gymnothorax moringa; Lethrinus atkinsoni; Hippoglossina oblonga; Scophthalmus aquosus; Urophycis tenuis; Centropristis striata; Caloenas nicobarica; Gallicolumba; Amandava subflava; Euplectes; Furcifer pardalis; Choerodon fasciatus; Coracias garrulus; Pisaster giganteus; Pleurogrammus monopterygius; Erpeton; Glyptocephalus zachirus; Philomachus; Zamenis longissimus; Coronella austriaca; Clavelina picta; Ascidiella aspersa; Thyonella gemmata; Mungos mungo; Accipiter nisus; Laemanctus; Neurergus; Fistularia commersonii; Cygnus cygnus; Diodon hystrix; Tamiops; Canis lupus lycaon; Amblyglyphidodon leucogaster; Euplectes orix; Anoplopoma fimbria; Chromis punctipinnis; Haemulon flavolineatum; Uromastyx ocellata; Stichopus chloronotus; Trachyphonus erythrocephalus; Coris gaimard; Labroides bicolor; Semicossyphus pulcher; Cuora mccordi; Amazona agilis; Dinemellia; Histrio histrio; Eumyias panayensis; Hemisphaeriodon; Zenopsis conchifer; Rhinecanthus aculeatus; Halocynthia pyriformis; Pytilia melba; Uraeginthus bengalus; Phloeomys; Cuora mouhotii; Merops apiaster; Pseudanthias; Potamochoerus porcus; Hemilepidotus jordani; Triglops scepticus; Bathymaster signatus; Ambystoma andersoni; Oxylebius pictus; Ecteinascidia turbinata; Malacochersus; Pachyuromys; Tockus flavirostris; Pseudobalistes fuscus; Taurotragus; Holothuria atra; Cyanoliseus patagonus; Ostorhinchus aureus; Sebastes semicinctus; Zaprora silenus; Podothecus accipenserinus; Platax teira; Cephalopholis miniata; Falco cherrug; Trachemys scripta scripta; Aotidae; Saimiriinae; Pseudomonacanthus peroni; Sebastes borealis; Sebastes chrysomelas; Sebastes norvegicus; Lutjanus quinquelineatus; Pterocaesio marri; Pitta moluccensis; Notamacropus parma; Camelus ferus; Dracaena guianensis; Lepidopsetta polyxystra; Oxycheilinus digramma; Giraffa giraffa; Ptilinopus pulchellus; Pleoticus muelleri; Lamprotornis chalcurus; Aonyx cinereus; Merops bullockoides; Chiroxiphia pareola; Ovis orientalis; Geopelia placida; Ammodytes hexapterus; Sufflamen chrysopterum; Sphoeroides maculatus; Cyclopsitta diophthalma; Astrochelys yniphora; Photoblepharon palpebratum; Boltenia ovifera; Centropyge heraldi; Rhabdamia gracilis; Parupeneus spilurus; Calyptocephallela gayi; Chrysopelea; Scolopsis bilineata; Pristigenys alta; Atherinomorus vaigiensis; Boltenia echinata; Echinarachnius parma; Vermilingua; Folivora; Lethenteron camtschaticum; Leptoclinus maculatus; Alitta succinea; Callocephalon fimbriatum; Bodianus diana; Coris caudimacula; Cantherhines pardalis; Salvelinus umbla; Gadus chalcogrammus; Doryteuthis pealeii; Holothuria cinerascens; Ophiopteris papillosa; Cheilodipterus quinquelineatus; Tetrastes bonasia; Grus paradisea; Parapercis xanthozona; Lyrurus tetrix; Ophiothrix spiculata; Ammodytes dubius; Cryptacanthodes maculatus; Lumpenus lampretaeformis; Prionotus carolinus; Crocodylia; Rhyticeros narcondami; Pseudanthias ventralis; Xenagama wilmsi; Ostorhinchus rueppellii; Ostorhinchus moluccensis; Loweina rara; Coracias cyanogaster; Vanellus armatus; Oxycercichthys veliferus; Ophioderma panamensis; Onuxodon fowleri; Cirrhilabrus roseafascia; Apostichopus parvimensis; Copsychus malabaricus; Notamacropus rufogriseus; Cirrhilabrus lineatus; Hypanus americanus; Cyanoloxia brissonii; Lonchura oryzivora; Leptoptilos crumenifer; Tockus alboterminatus; Tockus nasutus; Cheilopogon californicus
Experiment type Methylation profiling by high throughput sequencing
Summary We mapped DNA methylation in 580 animal species (535 vertebrates, 45 invertebrates), resulting in 2443 genome-scale, base-resolution DNA methylation profiles of primary tissue samples from various organs. Reference-genome independent analysis of this comprehensive dataset defined a “genomic code” of DNA methylation, which allowed us to predict global and locus-specific DNA methylation from the DNA sequence within and across species. This code appears broadly conserved throughout vertebrate evolution, with two major transitions – once in the first vertebrates and again with the emergence of reptiles. Beyond the central role of species-specific DNA sequence composition, our dataset identified the tissue type and the individual as two main sources of DNA methylation variability within species. Tissue type was the dominant factor in fish, birds, and mammals, while in invertebrates, reptiles, and amphibians both factors were similarly strong. Cross-species comparisons focusing on heart and liver tissues supported a highly conserved role of DNA methylation for tissue type and identity and cross-mapping based promoter methylation analysis revealed divergence at specific genes. In summary, this study establishes a large resource of vertebrate and invertebrate DNA methylomes, it showcases the power of reference-free epigenome analysis in species for which no reference genomes are available, and it contributes an epigenetic perspective to the study of vertebrate evolution.
 
Overall design Dataset comprises 2443 DNA methylation profiles (RRBS) covering 580 animal species (535 vertebrates and 45 invertebrates) and more than 10 major tissue types with a foucs on heart and liver, analysed in a reference-free manner.
Web link http://cross-species-methylation.computational-epigenetics.org
 
Contributor(s) Klughammer J, Romanovskaia D, Nemc A, Posautz A, Seid C, Schuster LC, Keinath MC, Lugo Ramos JS, Kosack L, Evankow A, Prinz D, Kirchberger S, Ergüner B, Datlinger P, Fortelny N, Schmidl C, Farlik M, Skjærven K, Bergthaler A, Liedvogel M, Thaller D, Burger PA, Hermann M, Distel M, Distel DL, Kübber-Heiss A, Bock C
Citation(s) 36646694
Submission date Feb 01, 2022
Last update date Feb 03, 2023
Contact name Christoph Bock
E-mail(s) cbock@cemm.oeaw.ac.at
Organization name CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences
Street address Lazarettgasse 14
City Vienna
ZIP/Postal code 1090
Country Austria
 
Platforms (580)
GPL21493 Illumina HiSeq 3000 (Mus musculus)
GPL22626 Illumina HiSeq 3000 (Gallus gallus)
GPL23274 Illumina HiSeq 3000 (Danio rerio)
Samples (3023)
GSM5852394 BC_3_Gran
GSM5852395 BC_3_Leuc
GSM5852396 PAO_3_G
Relations
BioProject PRJNA802599
SRA SRP357738

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
GSE195869_RAW.tar 54.4 Gb (http)(custom) TAR (of BED)
GSE195869_consensus_reference_fasta_files.tar.gz 13.0 Gb (ftp)(http) TAR
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record
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