GEO Browser - GEO

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96 series

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Accession	Title	Series type(s)	Organism(s)	Samples	Supplementary	Contact	Release date
Filter			Danio rerio		BED
GSE256288	Uncoupled H3K9me3 nucleation and reinforcement during early zebrafish embryogenesis	Genome binding/occupancy profiling by high throughput sequencing	Danio rerio	57	BED BW	Mary Goll	Jul 22, 2024
GSE233198	Differential programs of melanocyte cell states	Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing	Danio rerio Homo sapiens Mus musculus	20	BED BW MTX NARROWPEAK TBI TSV	Vivek T Natarajan	Jul 05, 2024
GSE268283	tp53 R217H and R242H Mutant Zebrafish Display Dysfunctional p53 Hallmarks and Recapitulate LFS Phenotypes [WGBS]	Methylation profiling by high throughput sequencing	Danio rerio	12	BED TXT	Kim Kobar	May 29, 2024
GSE267332	Integration of ATAC and RNA-Sequencing identifies chromatin and transcriptomic signatures in classical and non-classical zebrafish osteoblasts and indicates mechanisms of entpd5a regulation [ATAC]	Genome binding/occupancy profiling by high throughput sequencing	Danio rerio	12	BED	Kleio Petratou-Busswinkel	May 14, 2024
GSE250267	EVOLUTIONARY CO-OPTION OF AN ANCESTRAL CLOACAL REGULATORY LANDSCAPE WITH THE EMERGENCE OF DIGITS AND GENITALS	Genome binding/occupancy profiling by high throughput sequencing Other Expression profiling by high throughput sequencing	Danio rerio Mus musculus	34	BED BW COOL NARROWPEAK TXT	Aurelie Hintermann	Apr 17, 2024
GSE243256	Mapping the chromatin accessibility landscape of zebrafish embryogenesis at single-cell resolution by SPATAC-seq	Genome binding/occupancy profiling by high throughput sequencing	Danio rerio	535	BED BW XLSX	Keyong Sun	Apr 14, 2024
GSE215987	Single-cell chromatin landscape of non-myocytes reveals AP-1 as a key transcriptional regulator contributing to highly cooperative networks among non-myocyte subtypes during zebrafish heart regeneration [Cut&Tag]	Other	Danio rerio	4	BED	LI QIAN	Feb 26, 2024
GSE215988	Single-cell chromatin landscape of non-myocytes reveals AP-1 as a key transcriptional regulator contributing to highly cooperative networks among non-myocyte subtypes during zebrafish heart regeneration	Genome binding/occupancy profiling by high throughput sequencing Other	Danio rerio	12	BED	LI QIAN	Feb 26, 2024
GSE232043	Construction of zebrafish chromatin accessibility landscape at a single-cell level using CH-ATAC-seq	Genome binding/occupancy profiling by high throughput sequencing	Danio rerio	8	BED	Guoji Guo	Jan 15, 2024
GSE232162	Construction of a cross-species chromatin accessibility landscape at a single-cell level using CH-ATAC-seq	Genome binding/occupancy profiling by high throughput sequencing	Danio rerio Drosophila melanogaster Eisenia andrei	13	BED	Guoji Guo	Jan 15, 2024
GSE250450	CUT&RUN profiling of Tfap2a binding genome-wide using zebrafish embryos at 24hpf	Other	Danio rerio	2	BED BIGWIG	Colin Kenny	Dec 18, 2023
GSE217063	Shigella induces epigenetic reprogramming of zebrafish neutrophils	Genome binding/occupancy profiling by high throughput sequencing	Danio rerio	12	BED BIGWIG XLSX	Serge Mostowy	Sep 13, 2023
GSE232842	Unraveling the whole genome DNA methylation profile of zebrafish kidney marrow through Oxford Nanopore sequencing	Methylation profiling by high throughput sequencing	Danio rerio	12	BED	Xudong Liu	May 19, 2023
GSE182714	Adar-mediated A-to-I editing is required for establishment of embryonic body axes in zebrafish	Expression profiling by high throughput sequencing Other	Danio rerio	32	BED TSV XLSX SRA Run Selector	Cecilia Lanny Winata	Aug 02, 2022
GSE192947	A regulatory network of Sox and Six transcription factors initiate a cell fate transformation during hearing regeneration in adult zebrafish	Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing	Danio rerio	29	BED CSV H5 TBI	Erin Jimenez	Jul 19, 2022
GSE195869	Comparative analysis of genome-scale, base-resolution DNA methylation profiles across 580 animal species	Methylation profiling by high throughput sequencing	Abronia anzuetoi Acanthosaura Acanthurus triostegus Accipiter gentilis Accipiter nisus Acinonyx Acomys Acryllium vulturinum Agapornis Agapornis canus Agapornis lilianae Agapornis personatus Agapornis taranta Ailurus fulgens Alectis ciliaris Alitta succinea Amandava subflava Amazona Amazona agilis Amblyglyphidodon leucogaster Ambystoma Ambystoma andersoni Ambystoma mexicanum Ammodytes dubius Ammodytes hexapterus Ammotragus Anas platyrhynchos Anoplopoma fimbria Antidorcas Antilope Aonyx cinereus Aotidae Apodemus flavicollis Apodemus sylvaticus Apostichopus parvimensis Aptenodytes patagonicus Aquila heliaca Ara Ara ararauna Ardea Ariopsis felis Ascidiella aspersa Asio otus Astrochelys radiata Astrochelys yniphora Athene noctua Atherinomorus vaigiensis Axis axis Balearica pavonina Bathymaster signatus Batoidea Bison bonasus Boa constrictor Bodianus diana Boltenia echinata Boltenia ovifera Bos Boselaphus tragocamelus Bothriechis schlegelii Botryllus schlosseri Brachylophus Branchiostoma floridae Bubalus Bubo bubo Buteo Buteo buteo Buteo lagopus Bycanistes bucinator Cacatua alba Caiman yacare Callithrix jacchus Callocephalon fimbriatum Callorhinchus milii Caloenas nicobarica Calyptocephallela gayi Camelus dromedarius Camelus ferus Canis aureus Canis lupus Canis lupus familiaris Canis lupus lycaon Cantherhines pardalis Capra Capra aegagrus Capreolus capreolus Capricornis Capromyidae Capromys pilorides Carcharias taurus Cariamidae Carollia perspicillata Castoridae Casuarius casuarius Caviidae Cebinae Centropomus robalito Centropristis striata Centropyge heraldi Cephalopholis miniata Cercopithecus Cervidae Cervus elaphus Cervus nippon Chaetodon lineolatus Chaetodon lunula Chamaeleo calyptratus Chamaeleonidae Charadriidae Chauna torquata Cheilodipterus quinquelineatus Cheilopogon californicus Chelydra serpentina Chiroxiphia pareola Chloris chloris Chloropsis Choerodon fasciatus Chromis punctipinnis Chrysopelea Ciconia ciconia Ciconiidae Ciona intestinalis Circus aeruginosus Circus cyaneus Cirrhilabrus lineatus Cirrhilabrus roseafascia Clavelina picta Clupea harengus Coccothraustes Coliiformes Colobus guereza Colobus polykomos Columba livia Columbidae Connochaetes Copsychus malabaricus Coracias cyanogaster Coracias garrulus Coris caudimacula Coris gaimard Cornufer guentheri Coronella austriaca Correlophus ciliatus Corucia zebrata Corvus Corvus corax Corvus corone Corvus frugilegus Coryphaenoides acrolepis Coturnix coturnix Coturnix delegorguei Cricetinae Cricetomyinae Cricetus Crocodylia Crotalus Cryptacanthodes maculatus Ctenochaetus striatus Cucumaria frondosa Cuora mccordi Cuora mouhotii Cyanoliseus patagonus Cyanoloxia brissonii Cyclopsitta diophthalma Cyclopterus lumpus Cyclura Cyclura cornuta Cygnus cygnus Cygnus melancoryphus Cynictis Cynomys Cynoscion regalis Cyprinus carpio Dama dama Danio rerio Dascyllus aruanus Dasypodidae Dendrocygna viduata Dinemellia Diodon hystrix Dolichotis Dolichotis patagonum Doryteuthis pealeii Dracaena guianensis Dromaius novaehollandiae Ducula bicolor Duttaphrynus melanostictus Echinarachnius parma Ecsenius Ecteinascidia turbinata Elephas maximus indicus Eliomys quercinus Elops affinis Embiotoca jacksoni Emydidae Equus Equus asinus asinus Equus zebra Erethizon Erinaceidae Erpeton Erythrura Esox lucius Eudyptes chrysocome Eumyias panayensis Eunectes Euplectes Euplectes orix Eurypygidae Falco cherrug Falco peregrinus Falco tinnunculus Felis catus Felis silvestris Fistularia commersonii Folivora Fromia Fromia indica Furcifer pardalis Gadus chalcogrammus Gadus morhua Galeocerdo cuvier Gallicolumba Gallus Gallus gallus Garrulus glandarius Gekkonidae Geochelone Geoemyda spengleri Geopelia placida Geronticus eremita Giraffa giraffa Glis glis Glyptocephalus cynoglossus Glyptocephalus zachirus Graptemys Grus japonensis Grus paradisea Gymnothorax moringa Gypaetus Haemulon flavolineatum Haliaeetus albicilla Haliaeetus leucocephalus Halichoeres trimaculatus Halocynthia pyriformis Heleophrynidae Heloderma Hemilepidotus jordani Hemisphaeriodon Hemitragus Hemitripterus americanus Heterocephalus Hippoglossina oblonga Hippoglossoides elassodon Hippoglossoides platessoides Hippotragus Hippotragus equinus Histrio histrio Holothuria Holothuria atra Holothuria cinerascens Homarus americanus Hoplobatrachus tigerinus Hydrochoerus hydrochaeris Hypanus americanus Hypselecara coryphaenoides Hystricidae Iguanidae Illex illecebrosus Incilius alvarius Irena puella Jacanidae Jaculus Kobus Kobus leche Labroides bicolor Laemanctus Lagostomus maximus Lama glama Lampropeltis Lamprotornis chalcurus Leiocephalus Lemur Leontocebus fuscicollis Leontopithecus Leontopithecus chrysomelas Lepas anatifera Lepidopsetta polyxystra Leptailurus Leptoclinus maculatus Leptoptilos crumenifer Lepus europaeus Lepus timidus Lethenteron camtschaticum Lethrinus atkinsoni Leucoraja erinaceus Leucoraja ocellata Lissemys punctata Loligo vulgaris Lonchura oryzivora Lophius piscatorius Loriculus galgulus Loweina rara Loweina terminata Lumpenus lampretaeformis Lutjanus mahogoni Lutjanus quinquelineatus Lutra lutra Lynx lynx Lyrurus tetrix Lytechinus variegatus Macaca Macaca silenus Macaca sylvanus Macropodidae Macropus Macroscelidea Macroscelides proboscideus Magallana gigas Malacochersus Marmota Martes foina Meles meles Melopsittacus Merops apiaster Merops bullockoides Milvus milvus Mimus polyglottos Molgula citrina Monacanthidae Morone saxatilis Mullus surmuletus Mungos mungo Muntiacus Mus musculus Musophaga Musophagidae Mustela Mustela putorius Mustelidae Mustelus canis Mya arenaria Myocastor coypus Myoxocephalus octodecemspinosus Myzopsetta ferruginea Naja Nanger dama Nardoa novaecaledoniae Nasua Natrix tessellata Nectariniidae Negaprion brevirostris Neoniphon sammara Neurergus Notamacropus parma Notamacropus rufogriseus Nothobranchius furzeri Nyctereutes Nymphicus hollandicus Octopus vulgaris Onuxodon fowleri Ophioderma panamensis Ophiopteris papillosa Ophiothrix spiculata Oplurus Oryctolagus cuniculus Osteoglossum bicirrhosum Ostorhinchus aureus Ostorhinchus moluccensis Ostorhinchus rueppellii Ostrea edulis Otaria Ovis aries Ovis orientalis Oxycercichthys veliferus Oxycheilinus digramma Oxylebius pictus Pachyuromys Panthera leo Panthera onca Panthera pardus Panthera tigris Papio Papio hamadryas Paracanthurus hepatus Paracirrhites forsteri Paralichthys dentatus Parapercis xanthozona Paroedura picta Parupeneus spilurus Parus major Passer domesticus Patiria miniata Pelecanus Pelecanus crispus Penaeus Perdix perdix Petauridae Petaurus breviceps Phalacrocorax carbo Phascolarctos cinereus Phasianus colchicus Philomachus Phloeomys Phocidae Phodopus campbelli Phoenicopteriformes Photoblepharon palpebratum Phyllopteryx taeniolatus Picus viridis Pisaster brevispinus Pisaster giganteus Pithecia pithecia Pitta moluccensis Platax teira Plegadis falcinellus Pleoticus muelleri Pleurogrammus monopterygius Ploceus cucullatus Podothecus accipenserinus Pogona barbata Pollachius virens Polychrus marmoratus Polypedates otilophus Pomacentrus coelestis Pomatomus saltator Pongo Potamochoerus porcus Prionotus carolinus Pristigenys alta Probosciger aterrimus Procyon lotor Psammomys obesus Psarisomus dalhousiae Pseudanthias Pseudanthias ventralis Pseudobalistes fuscus Pseudomonacanthus peroni Psittacus Pterocaesio marri Pteropus Ptilinopus Ptilinopus pulchellus Puma concolor Pycnonotus barbatus Python molurus Python regius Pythonidae Pytilia melba Rangifer tarandus Rattus norvegicus Rattus rattus Recurvirostra avosetta Rhabdamia gracilis Rhacophorus reinwardtii Rhea americana Rhinecanthus aculeatus Rhinocerotidae Rhinogobiops nicholsii Rhinoptera bonasus Rhyticeros narcondami Riftia pachyptila Rollulus Rupicapra rupicapra Saccoglossus kowalevskii Saguinus Saguinus imperator Saguinus mystax Saguinus oedipus Saimiriinae Salmo salar Salmo trutta Salvelinus alpinus Salvelinus umbla Sarcophilus Sauromalus Scandentia Scincidae Sciurus vulgaris Scolopsis bilineata Scophthalmus aquosus Scopus umbretta Scyliorhinus retifer Sebastes atrovirens Sebastes borealis Sebastes caurinus Sebastes chrysomelas Sebastes constellatus Sebastes hopkinsi Sebastes miniatus Sebastes mystinus Sebastes norvegicus Sebastes ovalis Sebastes paucispinis Sebastes semicinctus Sebastolobus alascanus Semicossyphus pulcher Serinus Shinisaurus crocodilurus Spatula querquedula Spermophilus Spheniscus humboldti Sphoeroides maculatus Spinus spinus Squalus acanthias Stenotomus chrysops Stichopus chloronotus Strigiformes Strix aluco Strix uralensis Strongylocentrotus droebachiensis Strongylocentrotus purpuratus Struthio camelus Sturnus vulgaris Styela montereyensis Sufflamen chrysopterum Suricata Sus scrofa Sus scrofa domesticus Sylvia atricapilla Tamias Tamiops Tapirus Taurotragus Tayassuidae Terrapene Testudinidae Testudo hermanni Testudo kleinmanni Tetrao urogallus Tetrastes bonasia Theloderma Theropithecus gelada Thunnus albacares Thyonella gemmata Tiliqua rugosa Tiliqua scincoides Tinca tinca Tockus alboterminatus Tockus deckeni Tockus flavirostris Tockus nasutus Trachemys Trachemys scripta elegans Trachemys scripta scripta Trachyphonus erythrocephalus Tragelaphus angasii Tragelaphus spekii Tragulus javanicus Triglops scepticus Tringa totanus Trioceros jacksonii Tupaia Upupa epops Uraeginthus bengalus Uromastyx Uromastyx ocellata Urophycis tenuis Ursus Ursus arctos Vanellus armatus Varanus Varanus exanthematicus Varanus gouldii Varecia Vermilingua Vicugna Vicugna pacos Vidua paradisaea Vipera ammodytes Vipera berus Vulpes vulpes Xenagama wilmsi Xiphias gladius Yangochiroptera Yinpterochiroptera Zamenis longissimus Zaprora silenus Zenopsis conchifer Zoarces americanus Zosteropidae	3023	BED SRA Run Selector	Christoph Bock	Jun 18, 2022
GSE189072	WGBS and RNA-seq of Danio rerio in HSPC generation	Expression profiling by high throughput sequencing Methylation profiling by high throughput sequencing	Danio rerio	34	BED CSV TXT SRA Run Selector	chao tang	May 10, 2022
GSE167579	Comparative 3D Genome Architecture in Vertebrates (Hi-C)	Other	Bos taurus Canis lupus familiaris Danio rerio Felis catus Gallus gallus Homo sapiens Macaca mulatta Mus musculus Oryctolagus cuniculus Ovis aries Rattus norvegicus	25	BED HDF5 XLS SRA Run Selector	Mengnan He	Apr 12, 2022
GSE167581	Comparative 3D Genome Architecture in Vertebrates	Expression profiling by high throughput sequencing Other	Bos taurus Canis lupus familiaris Danio rerio Felis catus Gallus gallus Homo sapiens Macaca mulatta Mus musculus Oryctolagus cuniculus Ovis aries Rattus norvegicus Sus scrofa	54	BED HDF5 XLS	Mengnan He	Apr 12, 2022
GSE166644	H3K27ac ChIP-seq analysis for zebrafish normal thymus and tumors driven by overexpression of human IRF4	Genome binding/occupancy profiling by high throughput sequencing	Danio rerio	14	BED BROADPEAK SRA Run Selector	Tze King Tan	Mar 14, 2022