GEO DataSets

(Submitter supplied) The evolution of innate behaviors is ultimately due to genetic variation likely acting in the nervous system. Gene regulation may be particularly important because it can evolve in a modular brain-region specific fashion through the concerted action of cis- and trans-regulatory changes. Here, to investigate transcriptional variation and its regulatory basis across the brain, we perform RNA sequencing (RNA-Seq) on ten brain subregions in two sister species of deer mice (Peromyscus maniculatus and P. more...

Organism:

Peromyscus maniculatus x Peromyscus polionotus; Peromyscus maniculatus; Peromyscus polionotus

Type:

Expression profiling by high throughput sequencing

5 related Platforms

191 Samples

Download data: TSV

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

Organism:

Danio rerio; Didelphis marsupialis; Peromyscus maniculatus; Tupaia chinensis; Callithrix jacchus; Ovis aries; Homo sapiens; Sus scrofa domesticus; Rhabdomys pumilio; Mustela putorius furo; Bos taurus; Anolis sagrei; Ictidomys tridecemlineatus

Type:

Expression profiling by high throughput sequencing

13 related Platforms

118 Samples

Download data

(Submitter supplied) The basic plan of the retina is conserved across vertebrates, yet species differ profoundly in their visual needs (Baden et al., 2020). One might expect that retinal cell types evolved to accommodate these varied needs, but this has not been systematically studied. Here, we generated and integrated single-cell transcriptomic atlases of the retina from 17 species: humans, two non-human primates, four rodents, three ungulates, opossum, ferret, tree shrew, a teleost fish, a bird, a reptile and a lamprey. more...

Organism:

Peromyscus maniculatus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33578

8 Samples

Download data: CSV

(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; 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; 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; Microtus maximowiczii; 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; Myodes rufocanus; Varecia rubra; Leptonycteris yerbabuenae; Eulemur rufus; Fukomys damarensis; Eulemur albifrons; Gerbillus cheesmani; Microgale drouhardi; Notamacropus rufogriseus; Nesogale talazaci; 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; Microtus fortis; 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) We used RNA-seq to estimate allelic expression bias in the embryonic tails of E12.5 and E14.5 Peromyscus maniculatus nubiterrae x bairdii. Samples are from F1 hybrids between forest (P.m.nubiterrae) and prairie (P.m.bairdii) with different numbers of caudal vertebrae.

Organism:

Peromyscus maniculatus nubiterrae x Peromyscus maniculatus bairdii

Type:

Expression profiling by high throughput sequencing

Platform:

GPL31121

8 Samples

Download data: FA, RESULTS

(Submitter supplied) We used RNA-seq to compare transcriptional profiles from the embryonic tails from E12.5–E15.5 Peromyscus maniculatus. Samples are from two ecotypes, forest (P.m.nubiterrae) and prairie (P.m.bairdii) with different numbers of caudal vertebrae.

Organism:

Peromyscus maniculatus bairdii; Peromyscus maniculatus nubiterrae

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL31117 GPL31116

35 Samples

Download data: MATRIX

(Submitter supplied) Mammals differ more than 100-fold in maximum lifespan. Here, we conducted comparative transcriptomics on 26 species with diverse lifespans. We identified thousands of genes with expression levels negatively or positively correlated with a species' maximum lifespan (Neg- or Pos-MLS genes). Neg-MLS genes are primarily involved in energy metabolism and inflammation. Pos-MLS genes show enrichment in DNA repair, microtubule organization, and RNA transport. more...

Organism:

Peromyscus maniculatus; Ondatra zibethicus; Hydrochoerus hydrochaeris; Ellobius lutescens; Cuniculus paca; Cricetulus barabensis; Blarina brevicauda; Tamiasciurus hudsonicus; Rattus rattus; Myocastor coypus; Heterocephalus glaber; Castor canadensis; Acomys russatus; Mesocricetus auratus; Mus musculus; Sciurus carolinensis; Tamias striatus; Neotoma cinerea; Condylura cristata; Fukomys damarensis; Marmota monax; Cavia porcellus; Octodon degus; Chinchilla lanigera; Scalopus aquaticus

Type:

Expression profiling by high throughput sequencing

25 related Platforms

522 Samples

Download data: TXT

(Submitter supplied) How evolution modifies complex, innate behaviors is largely unknown. Divergence in many morphological traits has been linked, at least in part, to cis-regulatory changes in gene expression, a pattern also observed for some behaviors in recently diverged populations. Given this, we compared the gene expression in the brains of two interfertile sister species of Peromyscus mice, including allele-specific expression (ASE) of their F1 hybrids, that show large and heritable differences in burrowing behavior. more...

Organism:

Peromyscus polionotus; Peromyscus maniculatus x Peromyscus polionotus; Peromyscus maniculatus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL31189 GPL25885 GPL31190

18 Samples

Download data: CSV

(Submitter supplied) Whole transcriptome RNA sequencing in primary fibroblasts of outbred Peromyscus maniculatus was generated to explore the degree of coordination in gene expression.

Organism:

Peromyscus maniculatus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26686

10 Samples

Download data: TXT

(Submitter supplied) Whole transcriptome RNA sequencing in brain tissue was generated to explore differences between young and old animals of two closely related species of deer mice (genus Peromyscus) that reportedly differ in their lifespans: P. leucopus that lives for up to 8 years and P. maniculatus that exhibits a lifespan of about 4 years.

Organism:

Peromyscus leucopus; Peromyscus maniculatus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL26686 GPL29708

24 Samples

Download data: TXT

(Submitter supplied) Whole genome sequencing was generated to perform single nucleotide polymorphism (SNP) variant calling.

Organism:

Peromyscus maniculatus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26686

16 Samples

Download data: CSV

(Submitter supplied) Analysis of gene expression can be challenging, especially if it involves genetically diverse populations that exhibit high variation in their individual expression profile. Despite this variation though, it is conceivable that in the same individuals a high degree of coordination is maintained between transcripts that belong to the same signaling modules and are associated with related biological functions. more...

Organism:

Peromyscus maniculatus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26686

6 Samples

Download data: CSV

(Submitter supplied) We compare fore- and mid-brain transcriptomes of reproductive males in monogamous and non-monogamous species pairs of Peromyscus mice, Microtus voles, parid songbirds, dendrobatid frogs, and Xenotilapia species of cichlid fishes. Our study provides evidence of a universal transcriptomic mechanism underlying the evolution of monogamy in vertebrates.

Organism:

Anthus spinoletta; Microtus ochrogaster; Oophaga pumilio; Xenotilapia ornatipinnis; Prunella modularis; Microtus pennsylvanicus; Peromyscus californicus; Xenotilapia spiloptera; Peromyscus maniculatus; Ranitomeya imitator

Type:

Expression profiling by high throughput sequencing

10 related Platforms

10 Samples

Download data: CSV, FASTA