GEO DataSets

(Submitter supplied) We performed single-cell transcriptome analysis (using MARS-seq) and accessible chromatin profiling (ATAC-seq) in Branchiostoma lanceolatum embryos (21 hours post-fertilization)

Organism:

Branchiostoma lanceolatum

Type:

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

Platform:

GPL29870

6 Samples

Download data: BEDGRAPH, TSV, XLSX

(Submitter supplied) We investigate tissue transcriptomic evolution across bilaterian animals by analyzing RNA-seq data from eight different tissues across twenty species.

Organism:

Tribolium castaneum; Aedes aegypti; Xenopus tropicalis; Cloeon dipterum; Bombyx mori; Drosophila melanogaster; Callorhinchus milii; Monodelphis domestica; Episyrphus balteatus; Branchiostoma lanceolatum; Danio rerio; Blattella germanica; Strongylocentrotus purpuratus; Octopus bimaculoides; Strigamia maritima

Type:

Expression profiling by high throughput sequencing

15 related Platforms

89 Samples

Download data: TSV

(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; 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; Mya arenaria; Loligo vulgaris; Strongylocentrotus droebachiensis; Holothuria; Ciona intestinalis; Leucoraja erinacea; Lophius piscatorius; Hemitripterus americanus; Cyclopterus lumpus; Thunnus albacares; Testudinidae; Varanus; Gekkonidae; 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; 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; 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

Type:

Methylation profiling by high throughput sequencing

580 related Platforms

3023 Samples

Download data: BED

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

Organism:

Branchiostoma lanceolatum; Xenopus tropicalis; Danio rerio; Ptychodera flava

Type:

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

4 related Platforms

75 Samples

Download data: TSV, TXT

(Submitter supplied) Signaling pathways control a large number of gene regulatory networks (GRNs) during animal development, acting as major tools for body plan formation. Remarkably, in contrast to the large number of transcription factors present in animal genomes, only a few of these pathways operate during development. Moreover, most of them are largely conserved along metazoan evolution. How evolution has generated a vast diversity of animal morphologies with such a limited number of tools is still largely unknown. more...

Organism:

Danio rerio; Branchiostoma lanceolatum

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21741 GPL24210

33 Samples

Download data: TXT

(Submitter supplied) Signaling pathways control a large number of gene regulatory networks (GRNs) during animal development, acting as major tools for body plan formation. Remarkably, in contrast to the large number of transcription factors present in animal genomes, only a few of these pathways operate during development. Moreover, most of them are largely conserved along metazoan evolution. How evolution has generated a vast diversity of animal morphologies with such a limited number of tools is still largely unknown. more...

Organism:

Branchiostoma lanceolatum; Danio rerio

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL24210 GPL21741

24 Samples

Download data: BED

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

Organism:

Branchiostoma lanceolatum

Type:

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

Platform:

GPL24210

16 Samples

Download data

(Submitter supplied) The goal of this projet was to identify genes differentially expressed between control and Activin-treated explants at two time points (gastrula and neurula stage)

Organism:

Branchiostoma lanceolatum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24210

8 Samples

Download data: TSV

(Submitter supplied) The goal of this projet was to identify genomic region showing differential accessibility between control and Activin-treated amphioxus explants at two time points (gastrula and neurula stage)

Organism:

Branchiostoma lanceolatum

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24210

8 Samples

Download data: BED

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

Organism:

Branchiostoma lanceolatum; Danio rerio; Strongylocentrotus purpuratus

Type:

Methylation profiling by high throughput sequencing; Other

5 related Platforms

31 Samples

Download data: BED, BW

(Submitter supplied) Using hMeDIP-seq we validated the single-base resolution hydroxymethylomes (ACE-seq) of sea urchin, lancelet and zebrafish embryos.

Organism:

Danio rerio; Branchiostoma lanceolatum; Strongylocentrotus purpuratus

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL25186 GPL23085 GPL30935

8 Samples

Download data: BW

(Submitter supplied) Using ACE-seq we investigated single-base resolution hydroxymethylomes of sea urchin, lancelet and zebrafish during development.

Organism:

Branchiostoma lanceolatum; Danio rerio; Strongylocentrotus purpuratus

Type:

Other

5 related Platforms

15 Samples

Download data: BED

(Submitter supplied) We investigated genome folding across the eukaryotic tree of life. We find four general manifestations of genome organization at chromosome-scale that each emerge and disappear repeatedly over the course of evolution. The submission represents chromosome-length Hi-C contact maps, architecture type and homolog separation analyses for 26 species across the tree of life, representing all subphyla of chordates, all 7 extant vertebrate classes, and 7 out of 9 major animal phyla, as well as plants and fungi.

Organism:

Saccharomyces cerevisiae; Drosophila melanogaster; Gallus gallus; Hypsibius dujardini; Lethenteron camtschaticum; Strongylocentrotus purpuratus; Ciona intestinalis; Pleurobrachia bachei; Acropora millepora; Python bivittatus; Triticum aestivum; Caenorhabditis elegans; Aplysia californica; Aedes aegypti; Culex quinquefasciatus; Homo sapiens; Muntiacus reevesi; Muntiacus muntjak; Arachis hypogaea; Agaricus bisporus; Branchiostoma lanceolatum; Xenopus laevis; Notamacropus eugenii; Pygocentrus nattereri; Cristatella mucedo; Clonorchis sinensis; Chiloscyllium punctatum

Type:

Other

30 related Platforms

32 Samples

Download data: BEDPE, FASTA, HIC, VCF, WIG

(Submitter supplied) 4C-seq experiments to study the evolution of the chromatin architecture of ancient gene regulatory blocks at the origin of vertebrates.

Organism:

Branchiostoma lanceolatum; Danio rerio; Mus musculus

Type:

Other

Platforms:

GPL20177 GPL13112 GPL14875

12 Samples

Download data: BEDGRAPH

(Submitter supplied) The brain requires complex mechanisms of genome regulation to encode and store behavioural information. In mammals, DNA methylation deposited at non-CG dinucleotides characterises brain epigenomes. However, it is unclear to what extent this non-canonical form of DNA methylation is evolutionarily conserved. To test this we profile brain cytosine methylation across the major vertebrate lineages, amphioxus, honeybee and octopus, finding that non-CG methylation in adult brain methylomes is restricted to vertebrates. more...

Organism:

Apis mellifera; Callorhinchus milii; Octopus bimaculoides; Gallus gallus; Ornithorhynchus anatinus; Lethenteron camtschaticum; Branchiostoma lanceolatum; Danio rerio; Monodelphis domestica

Type:

Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

9 related Platforms

11 Samples

Download data: CGMAP, TSV

(Submitter supplied) We compared the transcriptomes of Amphioxus (Branchiostoma lanceolatum) control and SU5402 treated embryos to define putative FGF signalling pathway target genes during somitogenesis. Embryos were treated with 50µM of SU5402 from 5.5hpf to 8.5hpf, 11.5hpf, and 14.5hpf or from 15hpf to 18hpf, 21hpf, 24hpf. Total RNA was extracted from control and treated embryos.

Organism:

Branchiostoma lanceolatum

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL25775 GPL20177

24 Samples

Download data: FASTA, TXT

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

Organism:

Branchiostoma lanceolatum; Danio rerio; Oryzias latipes

Type:

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

7 related Platforms

217 Samples

Download data: BED, BEDGRAPH, TXT

(Submitter supplied) What genomic changes led to the origin of vertebrates remains a mystery. On the one hand, animal evolution is thought to be driven mostly by changes in the cis-regulatory regions of a shared conserved and toolkit of developmental genes. On the other hand, vertebrates experienced two rounds of whole genome duplication (WGD) that increased their gene repertoire, particularly of regulatory genes controlling embryo development. more...

Organism:

Branchiostoma lanceolatum; Danio rerio; Oryzias latipes

Type:

Expression profiling by high throughput sequencing

4 related Platforms

81 Samples

Download data: TXT

(Submitter supplied) What genomic changes led to the origin of vertebrates remains a mystery. On the one hand, animal evolution is thought to be driven mostly by changes in the cis-regulatory regions of a shared conserved and toolkit of developmental genes. On the other hand, vertebrates experienced two rounds of whole genome duplication (WGD) that increased their gene repertoire, particularly of regulatory genes controlling embryo development. more...

Organism:

Branchiostoma lanceolatum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24206

7 Samples

Download data: BEDGRAPH

(Submitter supplied) What genomic changes led to the origin of vertebrates remains a mystery. On the one hand, animal evolution is thought to be driven mostly by changes in the cis-regulatory regions of a shared conserved and toolkit of developmental genes. On the other hand, vertebrates experienced two rounds of whole genome duplication (WGD) that increased their gene repertoire, particularly of regulatory genes controlling embryo development. more...

Organism:

Danio rerio; Branchiostoma lanceolatum; Oryzias latipes

Type:

Genome binding/occupancy profiling by high throughput sequencing

4 related Platforms

29 Samples

Download data: BED