GEO DataSets

(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; Myodes rufocanus; Varecia rubra; Leptonycteris yerbabuenae; Eulemur rufus; Fukomys damarensis; Eulemur albifrons; Gerbillus cheesmani; Microgale drouhardi; Notamacropus rufogriseus; Microtus oeconomus; 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; 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; 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; 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

Type:

Methylation profiling by array

Platform:

GPL28271

15043 Samples

Download data: CSV, DOCX, IDAT

(Submitter supplied) Archived skin samples collected during common bottlenose dolphin health assessments in Barataria Bay, LA from 2016 to 2017 were analyzed by RNA-seq to support and enhance the assessment of animal health. The transcriptomic data were analyzed in conjunction with the substantial pool of health and environmental data collected during health assessments to investigate the utility of transcriptomic data in overall assessment of dolphin health and/or as markers of specific health concerns.

Organism:

Tursiops truncatus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27600

28 Samples

Download data: XLSX

(Submitter supplied) Archived blood samples collected during common bottlenose dolphin health assessments in the northern Gulf of Mexico from 2013 to 2018 were analyzed by RNA-seq to support and enhance the assessment of animal health. The transcriptomic data were analyzed in conjunction with the substantial pool of health and environmental data collected during health assessments to investigate the utility of transcriptomic data in overall assessment of dolphin health and/or as markers of specific health concerns.

Organism:

Tursiops truncatus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27600

76 Samples

Download data: XLSX

(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:

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

Type:

Methylation profiling by genome tiling array

Platform:

GPL28271

545 Samples

Download data: IDAT, TXT

(Submitter supplied) Whole blood was collected as part of monthly veterinary checkups of bottlenose dolphins housed at Dolphing Quest in Waikoloa, Hawaii, USA. Gene expression from 5 samples was analyzed for comparison to the blood transcriptome of the beluga whale.

Organism:

Tursiops truncatus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21538

5 Samples

Download data: FASTA, XLSX

(Submitter supplied) Common bottlenose dolphins serve as sentinels for the health of their coastal environments as they are susceptible to health impacts from anthropogenic inputs through both direct exposure and food web magnification. Remote biopsy samples have been widely used to reveal contaminant burdens in free-ranging bottlenose dolphins, but do not address the health consequences of this exposure. To gain insight into whether remote biopsies can also identify health impacts associated with contaminant burdens, we employed RNA sequencing (RNA-seq) to interrogate the transcriptomes of remote skin biopsies from 116 bottlenose dolphins from the northern Gulf of Mexico and southeastern U.S. more...

Organism:

Tursiops truncatus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21538

116 Samples

Download data: TXT, XLSX

(Submitter supplied) As apex predators, cetaceans are recognized as sentinels for the health of marine ecosystems. The ability to identify the impacts of anthropogenic contamination on the health of a species requires long term monitoring to establish baseline health parameters. This makes health measurements that can be sampled from free ranging animals highly desirable. In the current study, we investigate the utility of skin gene expression profiling to monitor the physiological, health, and contaminant exposure status in bottlenose dolphins. more...

Organism:

Tursiops truncatus

Type:

Expression profiling by array

Platform:

GPL18797

94 Samples

Download data: TXT

(Submitter supplied) Four captive bottlenose dolpins housed in Kona, Hawaii, were serially sampled at approximately monthly intervals over the course of one year, in order to establish baseline information on the content and variation of the dolphin blood transcriptome.

Organism:

Tursiops truncatus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21538

31 Samples

Download data: FASTA, PDF, XLS, XLSX

(Submitter supplied) To assess the impact of emerging contaminats on dolphin transcriptome

Organism:

Tursiops truncatus

Type:

Expression profiling by array

Platform:

GPL17696

8 Samples

Download data: TXT

(Submitter supplied) To validate the oligo array and to investigate the impact of the environmental stressors on dolphin health at transcriptomic level

Organism:

Tursiops truncatus

Type:

Expression profiling by array

Platform:

GPL17696

73 Samples

Download data: TXT

(Submitter supplied) An 8X15k oligonucleotide microarray was developed consisting of 2334 E. glacialis probes and 2166 Tursiops truncatus probes and used to measure the transcriptome level effects of right whale kidney fibroblast cells exposed to cadmium. Cells were exposed to three concentrations of cadmium chloride (CdCl2) for three exposure times. Cells exposed to 10-6M CdCl2 for 4 hours and 24 hours showed upregulated genes involved in protection from metal toxicity, oxidative stress, protein renaturation, apoptosis inhibition, and several regulators of cellular processes. more...

Organism:

Eubalaena glacialis; Tursiops truncatus

Type:

Expression profiling by array

Platform:

GPL8963

12 Samples

Download data: TXT

(Submitter supplied) To determine what can the transcriptome tell us about populations of free-ranging bottlenose dolphins, Tursiops truncatus. Keywords: health assessment

Organism:

Tursiops truncatus

Type:

Expression profiling by array

Platform:

GPL6523

151 Samples

Download data: TXT

(Submitter supplied) Goal: To determine the effects of capture-release events in wild dolphins (Tursiops truncatus). Methods: An analysis of the Peripheral Blood Leukocyte (PBL) transcriptome was conducted on a group of 20 animals. The samples were collected in 2 different locations along the US east coast (Charleston, SC; Indian River Lagoon, FL) and 2 blood samples were collected for each dolphin 1) immediately after the capture event (*pre*) and 2) just before the animal was released (*post*). more...

Organism:

Tursiops truncatus

Type:

Expression profiling by array

Platform:

GPL3609

40 Samples

Download data: TXT

(Submitter supplied) 3 technical replicates from Wild Dolphin PBL Keywords: Immune and stress response analysis

Organism:

Tursiops truncatus

Type:

Expression profiling by array

Platform:

GPL3609

8 Samples

Download data

(Submitter supplied) Arrays of this design have barcodes that begin with 16028889 or 2528889. Orientation: Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent scanner (barcode on the left, DNA on the back surface, scanned through the glass), matching the FeatureNum output from Agilent's Feature Extraction software. Protocol: see manufacturer's web site at http://www.agilent.com/

Organism:

Tursiops truncatus

1 Series

94 Samples

Download data

(Submitter supplied) Arrays of this design have barcodes that begin with 16028889 or 2528889. Orientation: Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent scanner (barcode on the left, DNA on the back surface, scanned through the glass), matching the FeatureNum output from Agilent's Feature Extraction software. The ID column represents the Agilent Feature Extraction feature number. more...

Organism:

Tursiops truncatus

2 Series

81 Samples

Download data: TXT

(Submitter supplied) An 8X15k oligonucleotide microarray was developed consisting of 2334 E. glacialis probes and 2166 Tursiops truncatus probes. There are 3 spot replicates/probe on the array, along with Agilent control grid specific for 8X15K arrays. The Platform data table reflects a condensed representation of the array's replicate features. The full array layout representing all of the individual features is linked as a supplementary file at the foot of this record. more...

Organism:

Tursiops truncatus; Eubalaena glacialis

1 Series

12 Samples

Download data: TXT

(Submitter supplied) as described by Mancia et al.

Organism:

Tursiops truncatus

1 Series

151 Samples

Download data