GEO DataSets

(Submitter supplied) Comparisons of molecular phenotypes across primates provide unique information to understand human biology and evolution and single-cell RNA-seq CRISPR interference screens are a powerful approach to analyze them. Here, we generate and validate three human, three gorilla and two cynomolgus iPS cell lines that carry a dox-inducible KRAB-dCas9 construct in the AAVS1 locus. We show that despite variable expression levels of KRAB-dCas9 among lines, comparable downregulation of target genes and comparable phenotypic effects are observed in a single-cell RNA-seq CRISPR interference screen. more...

Organism:

Homo sapiens; Gorilla gorilla; Macaca fascicularis

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL34203 GPL30882 GPL34204

68 Samples

Download data: RDS, XLSX

(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; 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; 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; 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

Type:

Methylation profiling by array

Platform:

GPL28271

15043 Samples

Download data: CSV, DOCX, IDAT

(Submitter supplied) Brain development is exceptionally delayed in humans compared to nonhuman primates (NHPs), a finding often termed neoteny. Signatures of neoteny, including a protracted proliferation of apical and basal progenitors as well as a delay in physiological activity of mature neurons, have been revealed in part through the use of induced pluripotent stem cell (iPSC) modeling of primate neurogenesis. IPSC modeling is particularly useful when examining the molecular drivers of a cellular phenotype such as gene transcription. more...

Organism:

Gorilla; Pan paniscus; Macaca mulatta; Pan troglodytes; Homo sapiens

Type:

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

10 related Platforms

79 Samples

Download data: BED, BEDGRAPH, TXT

(Submitter supplied) Comparing the molecular and cellular properties among primates is crucial to better understand human evolution and biology. However, it is difficult or ethically even impossible to collect matched tissues from many primates, especially during development. An alternative is to model different cell types and their development using induced pluripotent stem cells (iPSCs). These can be generated from many tissue sources, but non-invasive sampling would decisively broaden the spectrum of non-human primates that can be investigated. more...

Organism:

Homo sapiens; Gorilla gorilla; Pongo abelii

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL28987 GPL28986 GPL18460

42 Samples

Download data: TXT

(Submitter supplied) The protein-coding gene networks regulating heart development are well known. Less understood are the roles of long non-coding RNAs (lncRNAs), many of which are poorly conserved due to their origins from transposable elements (TEs) such as endogenous retroviruses (ERVs). Here, we report hundreds of ERV elements from the primate-specific MER41 family are expressed in pluripotent cell-derived cardiomyocytes and fetal heart, some of which are regulated by the cardiogenic transcription factor TBX5. more...

Organism:

Gorilla gorilla; Mus musculus; Homo sapiens; Macaca mulatta; Pan troglodytes

Type:

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

7 related Platforms

60 Samples

Download data: BW, HIC, TDF, TXT

(Submitter supplied) The human brain has undergone rapid expansion since humans diverged from other great apes, but the mechanism of this human-specific enlargement is still unknown. Here, we use cerebral organoids derived from human, gorilla and chimpanzee cells to study developmental mechanisms driving evolutionary brain expansion. We find that the differentiation of neuroepithelial cells to neurogenic radial glia is a protracted process in apes, involving a previously unrecognized transition state characterized by a change in cell shape. more...

Organism:

Homo sapiens; Gorilla gorilla

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL23656 GPL20301

42 Samples

Download data: TXT

(Submitter supplied) Here, we performed RNA-Seq on mRNA isolated from primary dermal fibroblasts of human, mice and multiple non-human primate species transfected with polyinosinic-polycytidylic acid (polyI:C), a synthetic dsRNA analog that invokes a strong interferon-mediated response, or mock transfected.

Organism:

Saimiri sciureus; Gorilla gorilla; Pongo abelii; Mus musculus; Pan paniscus; Macaca mulatta; Macaca nemestrina; Papio anubis; Homo sapiens; Pan troglodytes

Type:

Expression profiling by high throughput sequencing

14 related Platforms

197 Samples

Download data: TXT

(Submitter supplied) Evolution of transcriptional regulation is thought to be a major cause of the evolution of phenotypic traits. We compared DNase I Hypersensitive sites in fibroblast cells from five primates (human, chimpanzee, gorilla, orangutan, and macaque). We identified approximately 90,000 DHS sites, of which 59% are not significantly different between species, 27% are differential and likely due to a single evolutionary change, and 14% are differential and likely due to multiple changes. more...

Organism:

Macaca mulatta; Homo sapiens; Pan troglodytes; Gorilla gorilla; Pongo pygmaeus

Type:

Genome binding/occupancy profiling by high throughput sequencing

7 related Platforms

15 Samples

Download data: BED

(Submitter supplied) We developed a continuous-trait probabilistic model to identify genome-wide evolutionary patterns of 3D genome structures based on multi-species Hi-C data. We applied the proposed method to analyzing cross-species Hi-C data from the same cell type in multiple primate species. The results showed that the proposed method enables discovery of distinct Hi-C contact frequency evolutionary patterns across species.

Organism:

Pan troglodytes; Gorilla gorilla; Pan paniscus

Type:

Other

Platforms:

GPL19148 GPL24149 GPL24148

3 Samples

Download data: HIC, TXT

(Submitter supplied) Despite the substantial efforts made to compile the molecular maps of the human brain, they do not fully inform us of the features unique to humans. Yet, identification of these features might help us to understand both the evolution and nature of the human cognitive traits. Here, we approached this question by analyzing gene expression and H3K27ac chromatin modification data collected in eight brain regions of humans, chimpanzees, gorillas, gibbon and macaques. more...

Organism:

Hylobates lar; Gorilla gorilla; Pan troglodytes; Homo sapiens

Type:

Expression profiling by high throughput sequencing

7 related Platforms

107 Samples

Download data: TXT

(Submitter supplied) DNA methylation in sperm is among the most important factors shaping evolution of the mammalian genome. By directly altering germline mutation rates, the DNA methylation system has shaped the CpG landscape of mammalian genomes, resulting in the CpG island phenomenon. Yet little is known about how this system itself has co-evolved with its substrate during mammalian evolution. We analyzed full-genome single-CpG DNA methylation profiles in sperm from human, chimp, gorilla, rhesus, mouse, rat and dog. more...

Organism:

Canis lupus familiaris; Gorilla gorilla; Rattus norvegicus

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL18694 GPL16540 GPL21650

12 Samples

Download data: TXT

(Submitter supplied) Many loci in the human genome harbor complex genomic structures that can result in susceptibility to genomic rearrangements leading to various genomic disorders. Nephronophthisis 1 (NPHP1, MIM# 256100) is an autosomal recessive disorder that can be caused by defects of NPHP1; the gene maps within the human 2q13 region where low copy repeats (LCRs) are abundant. Loss of function of NPHP1 is responsible for approximately 85% of the NPHP1 cases - about 80% of such individuals carry a large recurrent homozygous NPHP1 deletion that occurs via non-allelic homologous recombination (NAHR) between two flanking directly oriented ~45 kb LCRs. more...

Organism:

Papio anubis; Pan troglodytes; Macaca mulatta; Gorilla gorilla; Pongo abelii; Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL21019

32 Samples

Download data: TXT

(Submitter supplied) Next Generation Sequencing of Unmethylated Alu (NSUMA) interrogation of more than 130,000 individual Alus for differential methylation with concomitant analysis of copy number variations applied to the study of hypomethylation in primates.

Organism:

Pan troglodytes; Pongo pygmaeus; Gorilla gorilla; Homo sapiens

Type:

Methylation profiling by high throughput sequencing

6 related Platforms

14 Samples

Download data: TXT

(Submitter supplied) Induced pluripotent stem cells (iPSCs) are regarded as a central tool to understand human biology in health and disease. Similarly, iPSCs from closely related species should be a central tool to understand human evolution and to identify conserved and variable patterns of iPSC disease models. Here, we have generated human, gorilla, bonobo and cynomolgus monkey iPSCs. We show that these cells are well comparable in their differentiation potential and generally similar to human, cynomolgus and rhesus monkey embryonic stem cells (ESCs). more...

Organism:

Macaca fascicularis; Pan paniscus; Macaca mulatta; Gorilla gorilla; Homo sapiens

Type:

Expression profiling by high throughput sequencing

5 related Platforms

23 Samples

Download data: TSV

(Submitter supplied) Only a minuscule fraction of long non-coding RNAs (lncRNAs) are well characterized. The evolutionary history of lncRNAs can provide insights into their functionality, but comparative analyses have been precluded by our ignorance of lncRNAs in non-model organisms. Here, we use RNA sequencing to identify lncRNAs in eleven tetrapod species and we present the first large-scale evolutionary study of lncRNA repertoires and expression patterns. more...

Organism:

Xenopus tropicalis; Macaca mulatta; Gorilla gorilla; Homo sapiens; Mus musculus; Gallus gallus; Ornithorhynchus anatinus; Monodelphis domestica

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

15 related Platforms

55 Samples

Download data: BEDGRAPH, TXT

(Submitter supplied) DNA methylation is an epigenetic modification involved in regulatory processes such as cell differentiation during development, X-chromosome inactivation, genomic imprinting and susceptibility to complex diseases. These changes can be inherited through generations and likely have played an important role during human evolution. We performed a comparative analysis of CpG methylation patterns between humans and all great apes (chimpanzee, bonobo, gorilla and orangutan) on a total of 32 individuals.Our analysis identified ~1,000 genes with significantly altered methylation patterns among the great apes, including ~200 with a methylation pattern unique to humans. more...

Organism:

Pongo pygmaeus; Homo sapiens; Pan troglodytes verus; Gorilla gorilla gorilla; Pongo abelii; Gorilla beringei graueri; Pan paniscus; Pan troglodytes schweinfurthii; Pan troglodytes troglodytes

Type:

Methylation profiling by array

Platform:

GPL13534

32 Samples

Download data: TXT

(Submitter supplied) The salamander microRNA expression between mid-bud limb regenerating blastemas (17 days post amputation) and non-regenerating stump tissues was compared by microarray analysis.

Organism:

Ambystoma mexicanum; Gorilla gorilla; Pan troglodytes; Bos taurus; Rattus norvegicus; Lemur catta; human gammaherpesvirus 4; JC polyomavirus; Human gammaherpesvirus 8; Betapolyomavirus macacae; Danio rerio; Ateles sp.; Homo sapiens; Monodelphis domestica; Betapolyomavirus hominis; Gallus gallus; Mus musculus; Human alphaherpesvirus 1; Human betaherpesvirus 5; Human immunodeficiency virus 1

Type:

Non-coding RNA profiling by array

Platforms:

GPL13686 GPL7724

7 Samples

Download data: TXT

(Submitter supplied) Gene expression differences are shaped by selective pressures and contribute to phenotypic differences between species. We identified 964 copy number differences (CNDs) of conserved sequences across 3 primate species and examined their potential effects on gene expression profiles. Samples with copy number different genes had significantly different expression than samples with neutral copy number. Genes encoding regulatory molecules differed in copy number and were associated with significant expression differences. Additionally, we identified 127 CNDs which were processed pseudogenes and some of which were expressed. Furthermore, there were copy number different regulatory regions such as ultraconserved elements and long intergenic noncoding RNAs with the potential to affect expression. We postulate that CNDs of these conserved sequences fine-tune developmental pathways by altering the levels of RNA.

Organism:

Pan troglodytes; Macaca mulatta; Homo sapiens; Pongo abelii; Gorilla beringei

Type:

Genome variation profiling by genome tiling array

Platform:

GPL14930

17 Samples

Download data: TXT

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

Organism:

Oryza sativa; Saccharum officinarum; Bombyx mori; Lemur catta; Lagothrix lagotricha; Macaca nemestrina; Homo sapiens; Canis lupus familiaris; Sus scrofa; Human betaherpesvirus 5; Monodelphis domestica; Takifugu rubripes; Populus trichocarpa; Glycine max; Medicago truncatula; Gallus gallus; Pan paniscus; Ovis aries; Murid gammaherpesvirus 4; Arabidopsis thaliana; Sorghum bicolor; Caenorhabditis briggsae; Caenorhabditis elegans; Anopheles gambiae; Drosophila melanogaster; Drosophila pseudoobscura; Apis mellifera; Xenopus laevis; Xenopus tropicalis; Ateles geoffroyi; Gorilla gorilla; Bos taurus; Mus musculus; Rattus norvegicus; Human gammaherpesvirus 8; Macacine gammaherpesvirus 4; Saguinus labiatus; Tetraodon nigroviridis; Physcomitrium patens; Zea mays; Danio rerio; Macaca mulatta; Pan troglodytes; Pongo pygmaeus; human gammaherpesvirus 4; Gallid alphaherpesvirus 2; Schmidtea mediterranea; Betapolyomavirus macacae

Type:

Expression profiling by array; Non-coding RNA profiling by array

Platforms:

GPL10558 GPL6844

16 Samples

Download data: GPR

(Submitter supplied) Background: Similar to replicating myoblasts, many rhabdomyosarcoma cells express the myogenic determination gene MyoD. In contrast to myoblasts, rhabdomyosarcoma cells do not make the transition from a regulative growth phase to terminal differentiation. Previously we demonstrated that the forced expression of MyoD with its E-protein dimerization partner was sufficient to induce differentiation and suppress multiple growth-promoting genes, suggesting that the dimer was targeting a switch that regulated the transition from growth to differentiation. more...

Organism:

Medicago truncatula; Sorghum bicolor; Zea mays; Caenorhabditis briggsae; Xenopus laevis; Xenopus tropicalis; Gallus gallus; Ateles geoffroyi; Mus musculus; Human gammaherpesvirus 8; Saguinus labiatus; Schmidtea mediterranea; Drosophila melanogaster; Drosophila pseudoobscura; Macaca nemestrina; Pan paniscus; Canis lupus familiaris; Ovis aries; Rattus norvegicus; Monodelphis domestica; Takifugu rubripes; Murid gammaherpesvirus 4; Physcomitrium patens; Populus trichocarpa; Glycine max; Bombyx mori; Lemur catta; Lagothrix lagotricha; Pan troglodytes; Sus scrofa; Human betaherpesvirus 5; human gammaherpesvirus 4; Betapolyomavirus macacae; Arabidopsis thaliana; Oryza sativa; Saccharum officinarum; Caenorhabditis elegans; Anopheles gambiae; Apis mellifera; Danio rerio; Macaca mulatta; Gorilla gorilla; Pongo pygmaeus; Homo sapiens; Bos taurus; Gallid alphaherpesvirus 2; Macacine gammaherpesvirus 4; Tetraodon nigroviridis

Type:

Non-coding RNA profiling by array

Platform:

GPL6844

4 Samples

Download data: GPR