GEO DataSets

(Submitter supplied) We performed 10× Genomics single-cell RNA sequencing on a mixed population of CD3+ PBMCs isolated from three healthy Large White pigs. Considering that cell resolution of scRNA-seq analysis can be improved based on large datasets, we also downloaded 7 pbulic PBMC scRNA-seq datasets using the same technique (10× Genomics). After rigorous quality control and the removal of batch effects, a total of 14,595 transcriptomes were obtained from 34,220 cells in 8 PBMC samples for subsequent analyses. more...

Organism:

Sus scrofa domesticus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL31437

1 Sample

Download data: MTX, TSV

(Submitter supplied) We found piRNAs with different lengths represented the predominant small RNA species in oocytes from the 12 explored species, except mouse. We found endo-siRNAs resulted from the truncated Dicer isoform were mouse-specific, and os-piRNAs associating with PIWIL3 in human oocytes are widespread in mammals and are typically with low levels of the 2’-3’-O-methylation. The sequences of many highly expressed piRNA clusters are fast-evolving compared with their syntenic genomic locations, and the TE families distributing in the conserved piRNA clusters are various between species.

Organism:

Macaca fascicularis; Oryctolagus cuniculus; Cricetulus griseus; Mesocricetus auratus; Mus musculus; Danio rerio; Homo sapiens; Canis lupus familiaris; Sus scrofa domesticus; Capra hircus; Rattus norvegicus; Cavia porcellus

Type:

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

12 related Platforms

138 Samples

Download data

(Submitter supplied) The development and migration of T cells in the thymus and peripheral tissues are crucial for maintaining adaptive immunity in mammals. However, the regulatory mechanisms underlying T cell development and thymocyte identity formation in pigs remain largely underexplored. Here, by integrating bulk and single-cell RNA-sequencing data, we investigated regulatory signatures of porcine thymus and lymph node T cells. more...

Organism:

Sus scrofa domesticus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19790

21 Samples

Download data: TXT

(Submitter supplied) Maintaining an appropriate concentration of vitamin D is essential for the proper functioning of the body regardless of age. Nowadays, there are more and more indications that vitamin D supplementation at higher than standard doses may show protective and therapeutic effects. Our study identifies differences in the body's response to long-term supplementation of cholecalciferol at an increased dose. more...

Organism:

Sus scrofa domesticus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL32212

16 Samples

Download data: XLSX

(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:

Sus scrofa domesticus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29562

11 Samples

Download data: CSV

(Submitter supplied) Maintaining an appropriate concentration of vitamin D is essential for the proper functioning of the body regardless of age. Nowadays, there are more and more indications that vitamin D supplementation at higher than standard doses may show protective and therapeutic effects. Our study identifies differences in the body's response to long-term supplementation of cholecalciferol at an increased dose. more...

Organism:

Sus scrofa domesticus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32212

9 Samples

Download data: XLSX

(Submitter supplied) Preterm Yorkshire piglets were provided parenteral nutrition for 14 days and developed cholestasis and histologic liver injury. Bottle-fed age-matched controls were provided sow milk replacer every 2-3 hours for 14 days.

Organism:

Sus scrofa domesticus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29562

9 Samples

Download data: XLSX

(Submitter supplied) Preterm Yorkshire piglets were provided parenteral nutrition for 14 days, receiving treatment with SEFA-6179 or a medium chain triglyceride vehicle control. At the end of 14 days, MCT piglets developed cholestasis and histologic liver injury.

Organism:

Sus scrofa domesticus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29562

11 Samples

Download data: TXT

(Submitter supplied) Introduction: Cardiac ischemic reperfusion injury (IRI) is paradoxically instigated by re-establishing blood-flow to ischemic myocardium typically from a myocardial infarction (MI). Although revascularization following MI remains the standard of care, effective strategies remain limited to prevent or attenuate IRI. We hypothesized that epicardial placement of human placental amnion/chorion (HPAC) grafts will protect against IRI. more...

Organism:

Sus scrofa domesticus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29562

27 Samples

Download data

(Submitter supplied) According to RNA-seq results, application of vitamin D in the form of 25(OH)D in swine diet can be beneficial for myogenesis, energy production and muscle fibre formation by influencing TOR signalling pathway. However, the use of vitamin D in the form of 25(OH)D may reduce muscle respiratory capacity.

Organism:

Sus scrofa domesticus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32212

34 Samples

Download data: TXT

(Submitter supplied) Objective The purpose of this study was to find the key regulatory genes and proteins in condylar ossification of temporomandibular joint (TMJ) by transcriptomics and proteomics in porcine embryos. Method A total of 12 miniature pig embryos (6 in each group) at E45 and E85 days were used in this study. Six embryos for tissue sections (3 in each group) . The remaining six embryos were cut down the condyle along the parallel line between the lowest point of the sigmoid notch and the highest point of the condyle, and each condylar tissue sample was divided into two parts averagely. more...

Organism:

Sus scrofa domesticus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29562

6 Samples

Download data: 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; 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; Mya arenaria; Loligo vulgaris; Strongylocentrotus droebachiensis; Holothuria; Ciona intestinalis; Leucoraja erinacea; Lophius piscatorius; Hemitripterus americanus; Cyclopterus lumpus; Thunnus albacares; Testudinidae; Varanus; Gekkonidae; 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; Pomatomus saltatrix; Ariopsis felis; Abronia anzuetoi; Eudyptes chrysocome; Pomacentrus coelestis; Terrapene; Lampropeltis; Embiotoca jacksoni; Geronticus eremita; Fromia indica; Ducula bicolor; Tockus nasutus; Rhinoptera bonasus; Probosciger aterrimus; Monacanthidae; Halichoeres trimaculatus; Phyllopteryx taeniolatus; Cyanocompsa brissonii; Tringa totanus; Chloropsis; Tockus alboterminatus; 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; Cheilopogon pinnatibarbatus californicus; Leptoclinus maculatus; Coris caudimacula; Gadus chalcogrammus; Doryteuthis pealeii; Crocodylia; Ophioderma panamensis; Notamacropus rufogriseus; Cirrhilabrus lineatus; 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; Leptoptilos crumeniferus; 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; 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; 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; Padda oryzivora; 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; 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

Type:

Methylation profiling by high throughput sequencing

580 related Platforms

3023 Samples

Download data: BED

(Submitter supplied) By leveraging single-cell/nuclei RNA sequencing, we generate the first single-cell transcriptome atlas of over 200,000 pig cells from 20 tissues/organs, as well as cultured ECs

Organism:

Sus scrofa domesticus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27926

2 Samples

Download data: MTX, TSV

(Submitter supplied) By leveraging single-cell/nuclei RNA sequencing, we generate the first single-cell transcriptome atlas of over 200,000 pig cells from 20 tissues/organs.

Organism:

Sus scrofa domesticus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL31246 GPL31247

45 Samples

Download data: MTX, TSV

(Submitter supplied) This study is designed to understand whether Pravastatin (Pra) treatment alters the transcriptome of small intestine after radiation injury. RNA was extracted from 15 Gy abdominal irradiated Gottingen minipigs with PS treatment. A cDNA library was generated using a TruSeq Stranded mRNA sample prep kit (Illumina, San Diego, CA), and transcriptome sequencing was performed using a TruSeq 3000/4000 SBS kit and Illumina sequencer with 101 bp paired-end reads per sample (Macrogen, Seoul, Korea).

Organism:

Sus scrofa domesticus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29562

6 Samples

Download data: TXT

(Submitter supplied) Single cell RNA sequencing was used to explore the long-term maintenance of immune memory cells and their functionality for the first time in this animal model. It revealed an increase in pertussis-specific T cells frequency in DTaP primed minipigs, together with up-regulation of genes involved in antigen presentation and interferon pathways.

Organism:

Sus scrofa domesticus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29562

6 Samples

Download data: MTX, TSV

(Submitter supplied) Here, we combine comparative regulatory genomics with machine learning to investigate enhancer logic in melanoma. Through epigenomics profiling of 26 melanoma cell lines across six species, we examine the conservation of the two main melanoma states and underlying master regulators. By training a deep neural network on topic models derived from the human lines, we were able to classify not only human melanoma enhancers, but also regulatory regions in the other species. more...

Organism:

Mus musculus; Danio rerio; Equus caballus; Homo sapiens; Canis lupus familiaris; Sus scrofa domesticus

Type:

Genome binding/occupancy profiling by high throughput sequencing

7 related Platforms

23 Samples

Download data: BW

(Submitter supplied) Reproductive performance of female pigs that do not receive sufficient colostrum from birth is permanently impaired. Whether lactocrine deficiency, reflected by low serum immunoglobulin immunocrit (iCrit), affects patterns of endometrial gene expression during the periattachment period of early pregnancy is unknown. Here, objectives were to determine effects of low iCrit at birth on the adult endometrial transcriptome on pregnancy day (PxD) 13. more...

Organism:

Sus scrofa domesticus

Type:

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

Platform:

GPL24919

30 Samples

Download data: XLSX

(Submitter supplied) Volumetric muscle loss (VML) resulting from extremity trauma presents chronic and persistent functional deficits which ultimately manifest disability. Acellular biological scaffolds, or decellularized extracellular matrices (ECMs), embody an ideal treatment platform due to their current clinical use for soft tissue repair, off-the-shelf availability, and zero autogenous donor tissue burden. ECMs have been reported to promote functional skeletal muscle tissue remodeling in small and large animal models of VML injury, and this conclusion was reached in a recent clinical trial that enrolled 13 patients. more...

Organism:

Sus scrofa domesticus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24919

12 Samples

Download data: TXT

(Submitter supplied) The aim of this study was to acquire a better understanding of porcine reproductive and respiratory syndrome (PRRS) disease through a deeper knowledge of gene expression changes that occur in pulmonary lymph nodes by comparing PRRS virus (PRRSV), porcine circovirus type 2 (PCV-2), and swine influenza virus (IAV-S) infections. The PRRSV, IAV-S and PCV-2 viral infections followed a clinical course in these domestic pigs typical of experimental infection of young pigs with these viruses. more...

Organism:

Sus scrofa domesticus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24684

16 Samples

Download data: TXT