GEO DataSets

(Submitter supplied) We study the genomic and developmental basis of the mammalian gliding membrane, or patagium, an adaptative trait that has repeatedly evolved in different lineages, including in closely related marsupial species. Through comparative genomic analysis of fifteen new marsupial genomes, both from gliding and non-gliding species, we find that the Emx2 locus experienced lineage-specific patterns of accelerated cis-regulatory evolution in gliding species. more...

Organism:

Macropus fuliginosus; Pseudochirops cupreus; Pseudochirops corinnae; Acrobates pygmaeus; Vombatus ursinus; Petaurus breviceps; Tarsipes rostratus; Distoechurus pennatus; Dactylopsila trivirgata; Pseudochirops archeri; Phalanger gymnotis; Petauroides volans; Pseudocheirus occidentalis; Macropus giganteus; Pseudocheirus peregrinus

Type:

Other

15 related Platforms

15 Samples

Download data: FASTA

(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:

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; 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; 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; 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; 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; 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; Craseomys rufocanus

Type:

Methylation profiling by array

Platform:

GPL28271

15043 Samples

Download data: CSV, DOCX, IDAT

(Submitter supplied) Here we describe the principles of 3D genome folding dynamics in vertebrates and show how lineage-specific patterns of genome reshuffling can result in different chromatin configurations. We (i) identified different patterns of chromosome folding across vertebrate species, (ii) reconstructed ancestral marsupial and afrotherian genomes analyzing whole-genome sequences of 10 species representative of the major therian phylogroups, (iii) detected lineage-specific chromosome rearrangements and (iv) identified the dynamics of the structural properties of genome reshuffling through therian evolution.

Organism:

Sarcophilus harrisii; Loxodonta africana; Notamacropus eugenii; Orycteropus afer

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other

7 related Platforms

15 Samples

Download data: BEDGRAPH, TSV, TXT

(Submitter supplied) 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. more...

Organism:

Riftia pachyptila; Homarus americanus; Pisaster brevispinus; Leucoraja erinaceus; Negaprion brevirostris; Danio rerio; Esox lucius; Gadus morhua; Myzopsetta ferruginea; Chelydra serpentina; Emydidae; Graptemys; Varanus exanthematicus; Naja; Vipera ammodytes; Dromaius novaehollandiae; Columba livia; Falco peregrinus; Haliaeetus albicilla; Serinus; Phalacrocorax carbo; Macropodidae; Erinaceidae; Leontocebus fuscicollis; Saguinus mystax; Cercopithecus; Vulpes vulpes; Ursus; Ursus arctos; Procyon lotor; Meles meles; Felis catus; Tayassuidae; Cervidae; Cervus nippon; Muntiacus; Ammotragus; Bos; Boselaphus tragocamelus; Bubalus; Cricetinae; Caviidae; Hydrochoerus hydrochaeris; Heterocephalus; Macroscelidea; Macroscelides proboscideus; Dolichotis; Duttaphrynus melanostictus; Corvus corone; Strigiformes; Vicugna pacos; Yinpterochiroptera; Acinonyx; Colobus guereza; Glyptocephalus cynoglossus; Erethizon; Nyctereutes; Trachemys; Stenotomus chrysops; Zosteropidae; Strix uralensis; Hippotragus; Vidua paradisaea; Cebinae; Phascolarctos cinereus; Leiocephalus; Carollia perspicillata; Milvus milvus; Cynomys; Psammomys obesus; Sylvia atricapilla; Python regius; Pogona barbata; Aquila heliaca; Eurypygidae; Jacanidae; Lissemys punctata; Ecsenius; Agapornis; Mimus polyglottos; Canis aureus; Tiliqua scincoides; Sebastes mystinus; Sebastes paucispinis; Ariopsis felis; Abronia anzuetoi; Eudyptes chrysocome; Pomacentrus coelestis; Terrapene; Lampropeltis; Embiotoca jacksoni; Geronticus eremita; Fromia indica; Ducula bicolor; Rhinoptera bonasus; Probosciger aterrimus; Monacanthidae; Halichoeres trimaculatus; Phyllopteryx taeniolatus; Tringa totanus; Chloropsis; Tockus deckeni; Chamaeleo calyptratus; Gymnothorax moringa; Centropristis striata; Erpeton; Laemanctus; Labroides bicolor; Cuora mccordi; Amazona agilis; Histrio histrio; Zenopsis conchifer; Uraeginthus bengalus; Bathymaster signatus; Pseudobalistes fuscus; Trachemys scripta scripta; Sebastes borealis; Lutjanus quinquelineatus; Lepidopsetta polyxystra; Oxycheilinus digramma; Giraffa giraffa; Pleoticus muelleri; Ovis orientalis; Geopelia placida; Photoblepharon palpebratum; Calyptocephallela gayi; Scolopsis bilineata; Atherinomorus vaigiensis; Leptoclinus maculatus; Coris caudimacula; Gadus chalcogrammus; Doryteuthis pealeii; Crocodylia; Ophioderma panamensis; Notamacropus rufogriseus; Cirrhilabrus lineatus; Lonchura oryzivora; Octopus vulgaris; Lytechinus variegatus; Squalus acanthias; Mustelus canis; Cyprinus carpio; Salmo salar; Salmo trutta; Pollachius virens; Zoarces americanus; Ambystoma; Iguanidae; Tiliqua rugosa; Natrix tessellata; Crotalus; Dendrocygna viduata; Charadriidae; Ciconia ciconia; Gallus; Coturnix coturnix; Parus major; Sarcophilus; Macropus; Tupaia; Lemur; Papio; Ailurus fulgens; Mustelidae; Lutra lutra; Mustela; Panthera onca; Panthera tigris; Rhinocerotidae; Cervus elaphus; Capra aegagrus; Connochaetes; Lepus europaeus; Marmota; Acomys; Mus musculus; Hystricidae; Melopsittacus; Tamias; Magallana gigas; Molgula citrina; Botryllus schlosseri; Heleophrynidae; Dama dama; Yangochiroptera; Leontopithecus; Pelecanus; Hippotragus equinus; Ostrea edulis; Cricetomyinae; Uromastyx; Cynictis; Glis glis; Oplurus; Bothriechis schlegelii; Brachylophus; Passer domesticus; Jaculus; Sauromalus; Python molurus; Acanthosaura; Shinisaurus crocodilurus; Plegadis falcinellus; Eliomys quercinus; Corvus corax; Coliiformes; Agapornis personatus; Loriculus galgulus; Leptailurus; Lepus timidus; Astrochelys radiata; Tragelaphus angasii; Sebastes constellatus; Sebastolobus alascanus; Paracanthurus hepatus; Corvus frugilegus; Dascyllus aruanus; Coryphaenoides acrolepis; Testudo hermanni; Paracirrhites forsteri; Scyliorhinus retifer; Nardoa novaecaledoniae; Chaetodon lineolatus; Chaetodon lunula; Buteo lagopus; Batoidea; Loweina terminata; Penaeus; Caiman yacare; Cacatua alba; Paroedura picta; Rhacophorus reinwardtii; Recurvirostra avosetta; Irena puella; Bycanistes bucinator; Elops affinis; Philomachus; Zamenis longissimus; Ascidiella aspersa; Tamiops; Amblyglyphidodon leucogaster; Rhinecanthus aculeatus; Hemilepidotus jordani; Triglops scepticus; Oxylebius pictus; Tockus flavirostris; Taurotragus; Cephalopholis miniata; Aotidae; Sebastes chrysomelas; Pterocaesio marri; Notamacropus parma; Lamprotornis chalcurus; Boltenia ovifera; Rhabdamia gracilis; Chrysopelea; Pristigenys alta; Salvelinus umbla; Holothuria cinerascens; Grus paradisea; Lyrurus tetrix; Ammodytes dubius; Cryptacanthodes maculatus; Prionotus carolinus; Ostorhinchus moluccensis; Apostichopus parvimensis; Cyanoloxia brissonii; Leptoptilos crumenifer; Illex illecebrosus; Strongylocentrotus purpuratus; Branchiostoma floridae; Galeocerdo cuvier; Callorhinchus milii; Clupea harengus; Salvelinus alpinus; Xiphias gladius; Ambystoma mexicanum; Heloderma; Casuarius casuarius; Rhea americana; Anas platyrhynchos; Ciconiidae; Columbidae; Accipiter gentilis; Circus aeruginosus; Acryllium vulturinum; Gallus gallus; Perdix perdix; Phasianus colchicus; Coturnix delegorguei; Spheniscus humboldti; Pteropus; Callithrix jacchus; Saguinus oedipus; Saguinus imperator; Macaca; Colobus polykomos; Pongo; Canis lupus; Panthera leo; Panthera pardus; Puma concolor; Tapirus; Sus scrofa domesticus; Camelus dromedarius; Lama glama; Tragulus javanicus; Capreolus capreolus; Rangifer tarandus; Ovis aries; Kobus; Capricornis; Oryctolagus cuniculus; Spermophilus; Cricetus; Rattus norvegicus; Rattus rattus; Amazona; Lynx lynx; Nymphicus hollandicus; Tinca tinca; Dolichotis patagonum; Incilius alvarius; Chauna torquata; Rollulus; Capromyidae; Vipera berus; Scopus umbretta; Rupicapra rupicapra; Pythonidae; Pelecanus crispus; Cucumaria frondosa; Coccothraustes; Polychrus marmoratus; Cygnus melancoryphus; Erythrura; Phodopus campbelli; Neoniphon sammara; Eunectes; Haliaeetus leucocephalus; Cariamidae; Macaca silenus; Musophagidae; Garrulus glandarius; Leontopithecus chrysomelas; Upupa epops; Paralichthys dentatus; Nanger dama; Myoxocephalus octodecemspinosus; Tragelaphus spekii; Sebastes ovalis; Hypselecara coryphaenoides; Spatula querquedula; Equus asinus asinus; Elephas maximus indicus; Falco tinnunculus; Tetrao urogallus; Testudo kleinmanni; Hoplobatrachus tigerinus; Musophaga; Osteoglossum bicirrhosum; Ptilinopus; Athene noctua; Polypedates otilophus; Correlophus ciliatus; Rhinogobiops nicholsii; Otaria; Leucoraja ocellata; Pycnonotus barbatus; Psarisomus dalhousiae; Cynoscion regalis; Acanthurus triostegus; Alectis ciliaris; Lethrinus atkinsoni; Hippoglossina oblonga; Scophthalmus aquosus; Gallicolumba; Amandava subflava; Furcifer pardalis; Choerodon fasciatus; Coronella austriaca; Thyonella gemmata; Neurergus; Diodon hystrix; Canis lupus lycaon; Euplectes orix; Chromis punctipinnis; Haemulon flavolineatum; Semicossyphus pulcher; Dinemellia; Aplonis panayensis; Hemisphaeriodon; Halocynthia pyriformis; Phloeomys; Cuora mouhotii; Merops apiaster; Pseudanthias; Ambystoma andersoni; Malacochersus; Cyanoliseus patagonus; Ostorhinchus aureus; Zaprora silenus; Platax teira; Saimiriinae; Pseudomonacanthus peroni; Sebastes norvegicus; Dracaena guianensis; Aonyx cinereus; Merops bullockoides; Ammodytes hexapterus; Sufflamen chrysopterum; Cyclopsitta diophthalma; Centropyge heraldi; Parupeneus spilurus; Vermilingua; Folivora; Lethenteron camtschaticum; Callocephalon fimbriatum; Ophiopteris papillosa; Ophiothrix spiculata; Rhyticeros narcondami; Ostorhinchus rueppellii; Lophoceros alboterminatus; Lophoceros nasutus; Cheilopogon californicus; Mya arenaria; Loligo vulgaris; Strongylocentrotus droebachiensis; Holothuria; Ciona intestinalis; Lophius piscatorius; Hemitripterus americanus; Cyclopterus lumpus; Thunnus albacares; Testudinidae; Varanus; Gekkonidae; Boa constrictor; Struthio camelus; Sturnus vulgaris; Phoenicopteriformes; Ara; Ara ararauna; Aptenodytes patagonicus; Petauridae; Dasypodidae; Scandentia; Varecia; Saguinus; Macaca sylvanus; Papio hamadryas; Theropithecus gelada; Canis lupus familiaris; Nasua; Martes foina; Mustela putorius; Felis silvestris; Phocidae; Equus; Equus zebra; Sus scrofa; Bison bonasus; Capra; Apodemus sylvaticus; Lagostomus maximus; Myocastor coypus; Saccoglossus kowalevskii; Psittacus; Castoridae; Styela montereyensis; Ardea; Buteo; Buteo buteo; Balearica pavonina; Grus japonensis; Corvus; Bubo bubo; Carcharias taurus; Axis axis; Vicugna; Hippoglossoides elassodon; Trachemys scripta elegans; Gypaetus; Morone saxatilis; Hippoglossoides platessoides; Capromys pilorides; Petaurus breviceps; Suricata; Hemitragus; Chloris chloris; Lepas anatifera; Chamaeleonidae; Lutjanus mahogoni; Circus cyaneus; Pithecia pithecia; Patiria miniata; Geochelone; Cyclura; Apodemus flavicollis; Sciurus vulgaris; Centropomus robalito; Cyclura cornuta; Cornufer guentheri; Antidorcas; Antilope; Kobus leche; Agapornis canus; Agapornis lilianae; Agapornis taranta; Varanus gouldii; Scincidae; Sebastes atrovirens; Sebastes caurinus; Sebastes hopkinsi; Sebastes miniatus; Geoemyda spengleri; Mullus surmuletus; Pomatomus saltator; Corucia zebrata; Picus viridis; Nothobranchius furzeri; Fromia; Asio otus; Strix aluco; Trioceros jacksonii; Theloderma; Nectariniidae; Ploceus cucullatus; Spinus spinus; Ctenochaetus striatus; Urophycis tenuis; Caloenas nicobarica; Euplectes; Coracias garrulus; Pisaster giganteus; Pleurogrammus monopterygius; Glyptocephalus zachirus; Clavelina picta; Mungos mungo; Accipiter nisus; Fistularia commersonii; Cygnus cygnus; Anoplopoma fimbria; Uromastyx ocellata; Stichopus chloronotus; Trachyphonus erythrocephalus; Coris gaimard; Pytilia melba; Potamochoerus porcus; Ecteinascidia turbinata; Pachyuromys; Holothuria atra; Sebastes semicinctus; Podothecus accipenserinus; Falco cherrug; Pitta moluccensis; Camelus ferus; Ptilinopus pulchellus; Chiroxiphia pareola; Sphoeroides maculatus; Astrochelys yniphora; Boltenia echinata; Echinarachnius parma; Alitta succinea; Bodianus diana; Cantherhines pardalis; Cheilodipterus quinquelineatus; Tetrastes bonasia; Parapercis xanthozona; Lumpenus lampretaeformis; Pseudanthias ventralis; Xenagama wilmsi; Loweina rara; Coracias cyanogaster; Vanellus armatus; Oxycercichthys veliferus; Onuxodon fowleri; Cirrhilabrus roseafascia; Copsychus malabaricus; Hypanus americanus

Type:

Methylation profiling by high throughput sequencing

580 related Platforms

3023 Samples

Download data: BED

(Submitter supplied) We investigated genome folding across the eukaryotic tree of life. We find four general manifestations of genome organization at chromosome-scale that each emerge and disappear repeatedly over the course of evolution. The submission represents chromosome-length Hi-C contact maps, architecture type and homolog separation analyses for 26 species across the tree of life, representing all subphyla of chordates, all 7 extant vertebrate classes, and 7 out of 9 major animal phyla, as well as plants and fungi.

Organism:

Saccharomyces cerevisiae; Drosophila melanogaster; Gallus gallus; Hypsibius dujardini; Lethenteron camtschaticum; Arachis hypogaea; Agaricus bisporus; Branchiostoma lanceolatum; Xenopus laevis; Notamacropus eugenii; Pygocentrus nattereri; Cristatella mucedo; Clonorchis sinensis; Chiloscyllium punctatum; Triticum aestivum; Caenorhabditis elegans; Aplysia californica; Aedes aegypti; Culex quinquefasciatus; Homo sapiens; Muntiacus reevesi; Muntiacus muntjak; Strongylocentrotus purpuratus; Ciona intestinalis; Pleurobrachia bachei; Acropora millepora; Python bivittatus

Type:

Other

30 related Platforms

32 Samples

Download data: BEDPE, FASTA, HIC, VCF, WIG

(Submitter supplied) We report transcriptome analysis of wallaby mammary epithelial cells (WallMEC) following treatment with mammary ECM from two distinct stages of lactation

Organism:

Notamacropus eugenii

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21832

4 Samples

Download data: FPKM_TRACKING

(Submitter supplied) We characterized the transcriptome of the wallaby placenta and lactating mammary gland over the course of reproduction

Organism:

Notamacropus eugenii

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL22742 GPL18017

13 Samples

Download data: TXT

(Submitter supplied) High throughput sequencing of miRNAs collected from tammar milk at different time points of lactation showed high levels of miRNA secreted in milk and allowed the identification of differentially expressed milk miRNAs during the lactation cycle as putative markers of mammary gland activity and functional candidate signals to assist growth and timed development of the young. Comparative analysis of miRNA distribution in milk and blood serum suggests that milk miRNAs are primarily expressed from mammary gland rather than transferred from maternal circulating blood, likely through a new putative exosomal secretory pathway.

Organism:

Notamacropus eugenii

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL18017

7 Samples

Download data: TXT

(Submitter supplied) In this study we use microarray technology to identify differentially expressed genes in the tammar wallaby mammary gland during the lactation cycle. We have focused on gene expression changes in the tammar mammary gland as it shifts from one lactation phase to the next.

Organism:

Notamacropus eugenii

Type:

Expression profiling by array

Platform:

GPL19466

96 Samples

Download data: TXT, XLS

(Submitter supplied) We collected (Illumina) RNA-seq data (polyadenylated RNA fraction) for a number of tissue samples from common marmoset and elephant. We developed a subtraction approach based on male/female RNA-seq data, Illumina genomic data and available genomes to identify and assemble Y transcripts. For marmoset samples, we added Y coding genes and noncoding sequences to the reference genomes in order to assess their expression levels. more...

Organism:

Callithrix jacchus; Rattus norvegicus; Notamacropus eugenii; Loxodonta africana

Type:

Expression profiling by high throughput sequencing

6 related Platforms

31 Samples

Download data: TXT

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

Organism:

Notamacropus eugenii

Type:

Non-coding RNA profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL14600 GPL13812

10 Samples

Download data: FASTA

(Submitter supplied) Chromatin immunoprecipitation from tammar wallaby pouch young cells for DNA bound to CENP-A

Organism:

Notamacropus eugenii

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL14600

2 Samples

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(Submitter supplied) Small RNA isolation of miRNAs, crasiRNAs and piRNAs for RNAseq from tammar wallaby pouch young

Organism:

Notamacropus eugenii

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13812

8 Samples

Download data: FASTA