GEO DataSets

(Submitter supplied) RNA viruses adapt rapidly to new host environments by generating highly diverse genome sets, so-called “quasispecies”. Minor genetic variants promote their rapid adaptation allowing for emergence of drug-resistance or immune-escape mutants. Understanding these adaptation processes is highly relevant to assess the risk of cross-species transmission, and safety and efficacy of vaccines and antivirals. more...

Organism:

Chlorocebus sabaeus; Mustela putorius furo; canine distemper virus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL34630 GPL34629

9 Samples

Download data: FASTA, WIG

(Submitter supplied) Vero cells, as approved by the World Health Organization, have been the most commonly used continuous cell line for viral vaccine production over the last 25 years, but their adherent phenotype continues to limit productivity. Adapting to a suspension culture would overcome this restriction and reduce production costs. First, a Vero suspension isolate was obtained and metabolically characterized. Second, RNA sequencing analysis was used to identify differentially expressed genes between adherent and suspension cells, which revealed complete downregulation of adhesion and matrix-associated genes. more...

Organism:

Chlorocebus sabaeus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28836

18 Samples

Download data: XLSX

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

Organism:

Chlorocebus sabaeus

Type:

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

Platforms:

GPL28836 GPL30937

36 Samples

Download data: BW

(Submitter supplied) Genomic DNA folds into complex configurations that produce particular local and globalstructures thought to profoundly impact genome function. To understand the dynamic nature ofthis relationship, we investigated the extent of host chromatin structural and functional changesin response to a viral agent. We performed comprehensive assessments of host architecture (Hi-C), accessibility (ATAC-seq), and gene expression (RNA-seq) in a paired manner in response toattenuated vaccinia (smallpox) virus. more...

Organism:

Chlorocebus sabaeus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28836

12 Samples

Download data: BW, CSV

(Submitter supplied) Genomic DNA folds into complex configurations that produce particular local and globalstructures thought to profoundly impact genome function. To understand the dynamic nature ofthis relationship, we investigated the extent of host chromatin structural and functional changesin response to a viral agent. We performed comprehensive assessments of host architecture (Hi-C), accessibility (ATAC-seq), and gene expression (RNA-seq) in a paired manner in response toattenuated vaccinia (smallpox) virus. more...

Organism:

Chlorocebus sabaeus

Type:

Other

Platform:

GPL30937

12 Samples

Download data: HIC

(Submitter supplied) Genomic DNA folds into complex configurations that produce particular local and globalstructures thought to profoundly impact genome function. To understand the dynamic nature ofthis relationship, we investigated the extent of host chromatin structural and functional changesin response to a viral agent. We performed comprehensive assessments of host architecture (Hi-C), accessibility (ATAC-seq), and gene expression (RNA-seq) in a paired manner in response toattenuated vaccinia (smallpox) virus. more...

Organism:

Chlorocebus sabaeus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL30937

12 Samples

Download data: BW

(Submitter supplied) Patterns of transcriptional activity are encoded in our genome through regulatory elements such as promoters or enhancers that, paradoxically, often contain similar assortments of sequence-specific transcription factor (TF) binding sites. Knowledge of how these sequence motifs encode multiple, often overlapping gene expression programs is central to understanding gene regulation and how mutations in non-coding DNA manifest in disease. more...

Organism:

Homo sapiens; Mus musculus; Chlorocebus sabaeus

Type:

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

4 related Platforms

56 Samples

Download data: BED, FA, TSV, TXT

(Submitter supplied) Nipah virus (NiV) is an emerging paramyxovirus which causes severe respiratory illness and deathly encephalitis in humans.Improving the ability of vaccines to induce strong, cellular, and humoral immune responses, remains the challenge to respond to Nipah and future Henipavirus infections rapidly and efficiently. A CD40.NiV vaccine has been engineered by fusing to the anti-CD40 monoclonal Ab the ectodomain of the Nipah G protein (Bangladesh strain) and immunogenic and conserved NiV F and N peptides. more...

Organism:

Chlorocebus sabaeus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18770

36 Samples

Download data: CSV

(Submitter supplied) Purpose: The global effort to combat COVID-19 rapidly produced a shortlist of approved drugs with anti-viral activities for clinical repurposing. However, the jump to clinical testing was lethal in some cases since a full understanding of the mechanism of antiviral activity as opposed to inherent toxicity for these drugs was lacking. We used parallel lipidomic and transcriptomic analyses to investigate the effect of Niclosamide (NIC), a poorly soluble anti-helminth drug identified for repurposed treatment of COVID-19, on SARS-CoV-2 infected Vero E6 cells. more...

Organism:

Chlorocebus sabaeus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28895

26 Samples

Download data: TAB

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

Organism:

Homo sapiens; Chlorocebus sabaeus

Type:

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

Platforms:

GPL24676 GPL28895

146 Samples

Download data: BW, SF, TXT

(Submitter supplied) COVID-19 remains a significant public health threat due to the ability of SARS-CoV-2 variants to evade the immune system and cause breakthrough infections. Although pathogenic coronaviruses such as SARS-CoV-2 and MERS-CoV lead to severe respiratory infections, how these viruses affect the chromatin proteomic composition upon infection remains largely uncharacterized. Here we used our recently developed integrative DNA And Protein Tagging (iDAPT) methodology to identify changes in host chromatin accessibility states and chromatin proteomic composition upon infection with pathogenic coronaviruses. more...

Organism:

Homo sapiens; Chlorocebus sabaeus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL28895 GPL24676

20 Samples

Download data: SF

(Submitter supplied) COVID-19 remains a significant public health threat due to the ability of SARS-CoV-2 variants to evade the immune system and cause breakthrough infections. Although pathogenic coronaviruses such as SARS-CoV-2 and MERS-CoV lead to severe respiratory infections, how these viruses affect the chromatin proteomic composition upon infection remains largely uncharacterized. Here we used our recently developed integrative DNA And Protein Tagging (iDAPT) methodology to identify changes in host chromatin accessibility states and chromatin proteomic composition upon infection with pathogenic coronaviruses. more...

Organism:

Homo sapiens; Chlorocebus sabaeus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL28895 GPL24676

114 Samples

Download data: BW

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

Organism:

Homo sapiens; Chlorocebus sabaeus

Type:

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

Platforms:

GPL28895 GPL21566 GPL20301

20 Samples

Download data: MTX, TSV

(Submitter supplied) Wet age-related macular degeneration (AMD), characterized by leaky neovessels emanating from the choroid, is a main cause of blindness. As current treatments for wet AMD require regular intravitreal injections of anti-VEGF biologics, there is a need for the novel development of less invasive treatments. Here, we developed a novel inhibitor of microtubule-associated End Binding 3 protein (EB3), herein termed EBIN, which blocked pathological Ca2+ signaling in activated endothelial cells and suppressed leakage of choroidal neovessels. more...

Organism:

Chlorocebus sabaeus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28895

6 Samples

Download data: MTX, TSV, TXT

(Submitter supplied) Wet age-related macular degeneration (AMD), characterized by leaky neovessels emanating from the choroid, is a main cause of blindness. As current treatments for wet AMD require regular intravitreal injections of anti-VEGF biologics, there is a need for the novel development of less invasive treatments. Here, we developed a novel inhibitor of microtubule-associated End Binding 3 protein (EB3), herein termed EBIN, which blocked pathological Ca2+ signaling in activated endothelial cells and suppressed leakage of choroidal neovessels. more...

Organism:

Chlorocebus sabaeus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL21566 GPL28895

4 Samples

Download data: BED, MTX, TSV, TXT

(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:

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; 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; 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; 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; Myodes rufocanus; Nothocricetulus migratorius

Type:

Methylation profiling by array

Platform:

GPL28271

15043 Samples

Download data: CSV, DOCX, IDAT

(Submitter supplied) DNA methylation data from vervet cerebral cortex, blood, and liver using highly conserved mammalian CpGs represented on the mammalian methylation array (HorvathMammalMethylChip40). We selected a total of 240 samples representing the entire vervet lifespan, from neonatal to senile stages: 144 samples from the peripheral blood, 48 samples from the liver, and 48 samples from the cortical brain area BA10.

Organism:

Homo sapiens; Chlorocebus sabaeus; Mus musculus; Rattus norvegicus

Type:

Methylation profiling by array

Platform:

GPL28271

240 Samples

Download data: CSV, DOCX, IDAT

(Submitter supplied) To investigate the SRCAP regulation of gene transcription during PRRSV infection, we established Marc-145 cell lines in which SRCAP gene has been knocked down by siRNA. We then performed gene expression profiling analysis using data obtained from RNA-seq.

Organism:

Chlorocebus sabaeus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28895

4 Samples

Download data: TXT

(Submitter supplied) The RNA modification N6-methyladenosine (m6A) plays a key role in the life cycles of several RNA viruses. Whether this applies to SARS-CoV-2 and whether m6A affects the outcome of COVID-19 disease is still poorly explored. Here we report that the RNA demethylase FTO strongly affects both m6A marking of SARS-CoV-2 and COVID-19 severity. By m6A profiling of SARS-CoV-2, we confirmed in infected cultured cells and showed for the first time in vivo in hamsters that the regions encoding TRS_L and the nucleocapsid protein are multiply marked by m6A, preferentially within RRACH motifs that are specific to β-coronaviruses and well conserved across SARS-CoV-2 variants. more...

Organism:

Chlorocebus sabaeus

Type:

Other

Platform:

GPL28836

12 Samples

Download data: BEDGRAPH

(Submitter supplied) We demonstrate that the histone demethylase KDM6A promotes infection of diverse coronaviruses, including SARS-CoV-1, SARS-CoV-2, MERS-CoV and mouse hepatitis virus (MHV) in a demethylase activity-independent manner

Organism:

Chlorocebus sabaeus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21566

4 Samples

Download data: TAB