Ascidian Network for In Situ Expression and Embryological Data

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Ascidian Network for In Situ Expression and Embryological Data

metasource: Fairsharing.org
version: FAIRsharing.org: ANISEED; Ascidian Network for In Situ Expression and Embryological Data; DOI: https://doi.org/10.25504/FAIRsharing.xp1x9c; Last edited: Sept. 17, 2019, 5:18 p.m.; Last accessed: Jan 03 2022 7:09 p.m.

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ANISEED

metasource: Fairsharing.org
version: FAIRsharing.org: ANISEED; Ascidian Network for In Situ Expression and Embryological Data; DOI: https://doi.org/10.25504/FAIRsharing.xp1x9c; Last edited: Sept. 17, 2019, 5:18 p.m.; Last accessed: Jan 03 2022 7:09 p.m.

metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:01.032409

metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:01.032409

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Other names: ANISEED

Aniseed is a database designed to offer a representation of ascidian embryonic development at the level of the genome (cis-regulatory sequences, spatial gene expression, protein annotation), of the cell (cell shapes, fate, lineage) or of the whole embryo (anatomy, morphogenesis).

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Publications: (8)

Publications

More detailed information about this field from each metasource. ×

The ANISEED database: digital representation, formalization, and elucidation of a chordate developmental program
PMID: 20647237

metasource: Fairsharing.org
version: FAIRsharing.org: ANISEED; Ascidian Network for In Situ Expression and Embryological Data; DOI: https://doi.org/10.25504/FAIRsharing.xp1x9c; Last edited: Sept. 17, 2019, 5:18 p.m.; Last accessed: Jan 03 2022 7:09 p.m.

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ANISEED 2017: extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets
PMID: 29149270

metasource: Fairsharing.org
version: FAIRsharing.org: ANISEED; Ascidian Network for In Situ Expression and Embryological Data; DOI: https://doi.org/10.25504/FAIRsharing.xp1x9c; Last edited: Sept. 17, 2019, 5:18 p.m.; Last accessed: Jan 03 2022 7:09 p.m.

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ANISEED 2015: a digital framework for the comparative developmental biology of ascidians
PMID: 26420834

metasource: Fairsharing.org
version: FAIRsharing.org: ANISEED; Ascidian Network for In Situ Expression and Embryological Data; DOI: https://doi.org/10.25504/FAIRsharing.xp1x9c; Last edited: Sept. 17, 2019, 5:18 p.m.; Last accessed: Jan 03 2022 7:09 p.m.

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http://dx.doi.org/10.1093/nar/gkx1108

metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:01.032409

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http://dx.doi.org/10.1093/nar/gkv966

metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:01.032409

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http://dx.doi.org/10.1101/gr.108175.110

metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:01.032409

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http://dx.doi.org/10.1016/j.cub.2005.12.044

metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:01.032409

---

http://dx.doi.org/10.1093/nar/gkz955

metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:01.032409

Close

• The ANISEED database: digital representation, formalization, and elucidation of a chordate developmental program PubMed citations: 51.

  51 articles citing: The ANISEED database: digital representation, formalization, and elucidation of a chordate developmental program

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  Spatiotemporal dynamics of single cell stiffness in the early developing ascidian chordate embryo. PMID:33727646

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  Phylogenetic comparison of egg transparency in ascidians by hyperspectral imaging. PMID:33257720

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  Phylogenetic Analyses of Glycosyl Hydrolase Family 6 Genes in Tunicates: Possible Horizontal Transfer. PMID:32823766

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  ANISEED 2019: 4D exploration of genetic data for an extended range of tunicates. PMID:31680137

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  From spiral cleavage to bilateral symmetry: the developmental cell lineage of the annelid brain. PMID:31640768

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  Differential Expression of a Classic Cadherin Directs Tissue-Level Contractile Asymmetry during Neural Tube Closure. PMID:31639367

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  Dynamic interplay of cell fate, polarity and force generation in ascidian embryos. PMID:30007244

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  ANISEED 2017: extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets. PMID:29149270

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  Functional and evolutionary insights from the Ciona notochord transcriptome. PMID:28928284

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  Proteomic responses to elevated ocean temperature in ovaries of the ascidian Ciona intestinalis. PMID:28500033

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  Generic Theoretical Models to Predict Division Patterns of Cleaving Embryos. PMID:27997824

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  Embryo Microinjection and Electroporation in the Chordate Ciona intestinalis. PMID:27805579

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  CardioTF, a database of deconstructing transcriptional circuits in the heart system. PMID:27635320

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  Quantifying Mosaic Development: Towards an Evo-Devo Postmodern Synthesis of the Evolution of Development via Differentiation Trees of Embryos. PMID:27548240

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  The Simple Chordate Ciona intestinalis Has a Reduced Complement of Genes Associated with Fanconi Anemia. PMID:27279728

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  Representation of anatomy in online atlases and databases: a survey and collection of patterns for interface design. PMID:27206491

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  TCF/Lef regulates the Gsx ParaHox gene in central nervous system development in chordates. PMID:26940763

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  A Boolean Function for Neural Induction Reveals a Critical Role of Direct Intercellular Interactions in Patterning the Ectoderm of the Ascidian Embryo. PMID:26714026

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  ACAM, a novel member of the neural IgCAM family, mediates anterior neural tube closure in a primitive chordate. PMID:26542009

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  ANISEED 2015: a digital framework for the comparative developmental biology of ascidians. PMID:26420834

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  Correlations Between the Morphology of Sonic Hedgehog Expression Domains and Embryonic Craniofacial Shape. PMID:26321772

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  Evolution of the chordate regeneration blastema: Differential gene expression and conserved role of notch signaling during siphon regeneration in the ascidian Ciona. PMID:26206613

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  A pipeline for the systematic identification of non-redundant full-ORF cDNAs for polymorphic and evolutionary divergent genomes: Application to the ascidian Ciona intestinalis. PMID:26025923

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  An organismal perspective on C. intestinalis development, origins and diversification. PMID:25807088

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  Bioadhesion in ascidians: a developmental and functional genomics perspective. PMID:25657840

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  Quantitative and in toto imaging in ascidians: working toward an image-centric systems biology of chordate morphogenesis. PMID:25262824

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  Divergent mechanisms regulate conserved cardiopharyngeal development and gene expression in distantly related ascidians. PMID:25209999

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  Fibroblast growth factor signalling controls nervous system patterning and pigment cell formation in Ciona intestinalis. PMID:25189217

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  An otx/nodal regulatory signature for posterior neural development in ascidians. PMID:25121599

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  Ephrin-mediated restriction of ERK1/2 activity delimits the number of pigment cells in the Ciona CNS. PMID:25062608

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  Islet is a key determinant of ascidian palp morphogenesis. PMID:24993943

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  Ontology for the asexual development and anatomy of the colonial chordate Botryllus schlosseri. PMID:24789338

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  Dissection of a Ciona regulatory element reveals complexity of cross-species enhancer activity. PMID:24680932

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  Towards 3D in silico modeling of the sea urchin embryonic development. PMID:24386014

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  Spatial expression of transcription factors in Drosophila embryonic organ development. PMID:24359758

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  NK4 antagonizes Tbx1/10 to promote cardiac versus pharyngeal muscle fate in the ascidian second heart field. PMID:24311985

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  Anterior-posterior regionalized gene expression in the Ciona notochord. PMID:24288133

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  Parallel evolution of chordate cis-regulatory code for development. PMID:24282393

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  Manteia, a predictive data mining system for vertebrate genes and its applications to human genetic diseases. PMID:24038354

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  Study of Cis-regulatory Elements in the Ascidian Ciona intestinalis. PMID:23997651

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  Endrov: an integrated platform for image analysis. PMID:23722203

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  Tbx2/3 is an essential mediator within the Brachyury gene network during Ciona notochord development. PMID:23674602

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  Progenitors of the protochordate ocellus as an evolutionary origin of the neural crest. PMID:23575111

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  Highly conserved elements discovered in vertebrates are present in non-syntenic loci of tunicates, act as enhancers and can be transcribed during development. PMID:23393190

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  Identification of a rudimentary neural crest in a non-vertebrate chordate. PMID:23135395

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  Genetic and genomic toolbox of the chordate Ciona intestinalis. PMID:22964837

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  Monoaminergic modulation of photoreception in ascidian: evidence for a proto-hypothalamo-retinal territory. PMID:22642675

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  FGF signaling establishes the anterior border of the Ciona neural tube. PMID:22627287

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  The identification of transcription factors expressed in the notochord of Ciona intestinalis adds new potential players to the brachyury gene regulatory network. PMID:21594950

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  Expression of the Distalless-B gene in Ciona is regulated by a pan-ectodermal enhancer module. PMID:21338600

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  The importance of being specified: cell fate decisions and their role in cell biology. PMID:21079016
• ANISEED 2017: extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets PubMed citations: 36.

  36 articles citing: ANISEED 2017: extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets

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  Highly distinct genetic programs for peripheral nervous system formation in chordates. PMID:35761237

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  Hmx gene conservation identifies the origin of vertebrate cranial ganglia. PMID:35585239

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  RSAT 2022: regulatory sequence analysis tools. PMID:35544234

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  Yamanaka Factors in the Budding Tunicate Botryllus schlosseri Show a Shared Spatio-Temporal Expression Pattern in Chordates. PMID:35342743

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  Amphioxus muscle transcriptomes reveal vertebrate-like myoblast fusion genes and a highly conserved role of insulin signalling in the metabolism of muscle. PMID:35105312

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  Xbp1 and Brachyury establish an evolutionarily conserved subcircuit of the notochord gene regulatory network. PMID:35049502

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  Developmental Table and Three-Dimensional Embryological Image Resource of the Ascidian Ascidiella aspersa. PMID:34977032

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  The Genome of the "Sea Vomit" Didemnum vexillum. PMID:34947908

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  JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles. PMID:34850907

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  Cardiopharyngeal deconstruction and ancestral tunicate sessility. PMID:34789899

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  Single-cell analysis of cell fate bifurcation in the chordate Ciona. PMID:34465302

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  The Ascidia Ciona robusta Provides Novel Insights on the Evolution of the AP-1 Transcriptional Complex. PMID:34414189

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  Neuromesodermal Lineage Contribution to CNS Development in Invertebrate and Vertebrate Chordates. PMID:33920662

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  Phylogenetic comparison of egg transparency in ascidians by hyperspectral imaging. PMID:33257720

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  Conservation of peripheral nervous system formation mechanisms in divergent ascidian embryos. PMID:33191918

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  A putative chordate luciferase from a cosmopolitan tunicate indicates convergent bioluminescence evolution across phyla. PMID:33082360

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  The Cis-Regulatory Code for Kelch-like 21/30 Specific Expression in Ciona robusta Sensory Organs. PMID:33043001

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  Rimbp, a New Marker for the Nervous System of the Tunicate Ciona robusta. PMID:32867148

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  Shotgun Proteomics of Ascidians Tunic Gives New Insights on Host-Microbe Interactions by Revealing Diverse Antimicrobial Peptides. PMID:32668814

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  Regulation of Neurogenesis by FGF Signaling and Neurogenin in the Invertebrate Chordate Ciona. PMID:32656209

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  Development of a high efficient promoter finding method based on transient transfection. PMID:32550544

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  More Than One-to-Four via 2R: Evidence of an Independent Amphioxus Expansion and Two-Gene Ancestral Vertebrate State for MyoD-Related Myogenic Regulatory Factors (MRFs). PMID:32520990

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  Transposon Reactivation in the Germline May Be Useful for Both Transposons and Their Host Genomes. PMID:32397241

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  The Spindle Assembly Checkpoint Functions during Early Development in Non-Chordate Embryos. PMID:32354040

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  MorphoSeq: Full Single-Cell Transcriptome Dynamics Up to Gastrulation in a Chordate. PMID:32315617

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  Dynamic Evolution of the Cthrc1 Genes, a Newly Defined Collagen-Like Family. PMID:32022859

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  Combinatorial chromatin dynamics foster accurate cardiopharyngeal fate choices. PMID:31746740

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  ANISEED 2019: 4D exploration of genetic data for an extended range of tunicates. PMID:31680137

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  Bioinformatics for Marine Products: An Overview of Resources, Bottlenecks, and Perspectives. PMID:31614509

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  Regulation and evolution of muscle development in tunicates. PMID:31249657

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  MorphoNet: an interactive online morphological browser to explore complex multi-scale data. PMID:31249294

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  WashU Epigenome Browser update 2019. PMID:31165883

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  Single-cell transcriptome profiling of the Ciona larval brain. PMID:30392840

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  Multiple inputs into a posterior-specific regulatory network in the Ciona notochord. PMID:30287118

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  Developmental system drift in motor ganglion patterning between distantly related tunicates. PMID:30062003

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  Wnt evolution and function shuffling in liberal and conservative chordate genomes. PMID:30045756
• ANISEED 2015: a digital framework for the comparative developmental biology of ascidians PubMed citations: 32.

  32 articles citing: ANISEED 2015: a digital framework for the comparative developmental biology of ascidians

  ×

  Mechanisms of Sperm-Egg Interactions: What Ascidian Fertilization Research Has Taught Us. PMID:35805180

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  Xbp1 and Brachyury establish an evolutionarily conserved subcircuit of the notochord gene regulatory network. PMID:35049502

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  Neuronal identities derived by misexpression of the POU IV sensory determinant in a protovertebrate. PMID:35042818

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  Developmental Table and Three-Dimensional Embryological Image Resource of the Ascidian Ascidiella aspersa. PMID:34977032

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  Stem Cells and Innate Immunity in Aquatic Invertebrates: Bridging Two Seemingly Disparate Disciplines for New Discoveries in Biology. PMID:34276677

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  CeLaVi: an interactive cell lineage visualization tool. PMID:33956141

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  Brachyury controls Ciona notochord fate as part of a feed-forward network. PMID:33419874

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  Transcription Factors of the bHLH Family Delineate Vertebrate Landmarks in the Nervous System of a Simple Chordate. PMID:33114624

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  In silico identification and functional validation of linear cationic α-helical antimicrobial peptides in the ascidian Ciona intestinalis. PMID:32724213

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  Three multi-allelic gene pairs are responsible for self-sterility in the ascidian Ciona intestinalis. PMID:32054881

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  ANISEED 2019: 4D exploration of genetic data for an extended range of tunicates. PMID:31680137

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  Positioning a multifunctional basic helix-loop-helix transcription factor within the Ciona notochord gene regulatory network. PMID:30661645

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  Neuronal identity: the neuron types of a simple chordate sibling, the tadpole larva of Ciona intestinalis. PMID:30530111

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  Developmental system drift in motor ganglion patterning between distantly related tunicates. PMID:30062003

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  Wnt evolution and function shuffling in liberal and conservative chordate genomes. PMID:30045756

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  A phylogenomic framework and timescale for comparative studies of tunicates. PMID:29653534

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  De novo draft assembly of the Botrylloides leachii genome provides further insight into tunicate evolution. PMID:29615780

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  ANISEED 2017: extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets. PMID:29149270

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  Hox gene cluster of the ascidian, Halocynthia roretzi, reveals multiple ancient steps of cluster disintegration during ascidian evolution. PMID:28932414

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  Functional and evolutionary insights from the Ciona notochord transcriptome. PMID:28928284

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  Evolutionary loss of melanogenesis in the tunicate Molgula occulta. PMID:28729899

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  Genome-wide survey of miRNAs and their evolutionary history in the ascidian, Halocynthia roretzi. PMID:28427349

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  Evaluation and rational design of guide RNAs for efficient CRISPR/Cas9-mediated mutagenesis in Ciona. PMID:28341547

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  The CNS connectome of a tadpole larva of Ciona intestinalis (L.) highlights sidedness in the brain of a chordate sibling. PMID:27921996

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  Bilaterian Giant Ankyrins Have a Common Evolutionary Origin and Play a Conserved Role in Patterning the Axon Initial Segment. PMID:27911898

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  Embryo Microinjection and Electroporation in the Chordate Ciona intestinalis. PMID:27805579

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  Ciona as a Simple Chordate Model for Heart Development and Regeneration. PMID:27642586

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  Automated detection of ncRNAs in the draft genome sequence of a colonial tunicate: the carpet sea squirt Didemnum vexillum. PMID:27576499

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  Representation of anatomy in online atlases and databases: a survey and collection of patterns for interface design. PMID:27206491

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  Old knowledge and new technologies allow rapid development of model organisms. PMID:26976934

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  The 2016 database issue of Nucleic Acids Research and an updated molecular biology database collection. PMID:26740669

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  Brachyury, Foxa2 and the cis-Regulatory Origins of the Notochord. PMID:26684323
• http://dx.doi.org/10.1093/nar/gkx1108
• http://dx.doi.org/10.1093/nar/gkv966
Show more
http://dx.doi.org/10.1101/gr.108175.110
http://dx.doi.org/10.1016/j.cub.2005.12.044
http://dx.doi.org/10.1093/nar/gkz955
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More detailed information about this field from each metasource. ×

curated information

metasource: Fairsharing.org
version: FAIRsharing.org: ANISEED; Ascidian Network for In Situ Expression and Embryological Data; DOI: https://doi.org/10.25504/FAIRsharing.xp1x9c; Last edited: Sept. 17, 2019, 5:18 p.m.; Last accessed: Jan 03 2022 7:09 p.m.

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gene

metasource: Fairsharing.org
version: FAIRsharing.org: ANISEED; Ascidian Network for In Situ Expression and Embryological Data; DOI: https://doi.org/10.25504/FAIRsharing.xp1x9c; Last edited: Sept. 17, 2019, 5:18 p.m.; Last accessed: Jan 03 2022 7:09 p.m.

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gene expression data

metasource: Fairsharing.org
version: FAIRsharing.org: ANISEED; Ascidian Network for In Situ Expression and Embryological Data; DOI: https://doi.org/10.25504/FAIRsharing.xp1x9c; Last edited: Sept. 17, 2019, 5:18 p.m.; Last accessed: Jan 03 2022 7:09 p.m.

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genome

metasource: Fairsharing.org
version: FAIRsharing.org: ANISEED; Ascidian Network for In Situ Expression and Embryological Data; DOI: https://doi.org/10.25504/FAIRsharing.xp1x9c; Last edited: Sept. 17, 2019, 5:18 p.m.; Last accessed: Jan 03 2022 7:09 p.m.

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life cycle stage

metasource: Fairsharing.org
version: FAIRsharing.org: ANISEED; Ascidian Network for In Situ Expression and Embryological Data; DOI: https://doi.org/10.25504/FAIRsharing.xp1x9c; Last edited: Sept. 17, 2019, 5:18 p.m.; Last accessed: Jan 03 2022 7:09 p.m.

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literature curation

metasource: Fairsharing.org
version: FAIRsharing.org: ANISEED; Ascidian Network for In Situ Expression and Embryological Data; DOI: https://doi.org/10.25504/FAIRsharing.xp1x9c; Last edited: Sept. 17, 2019, 5:18 p.m.; Last accessed: Jan 03 2022 7:09 p.m.

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mutation

metasource: Fairsharing.org
version: FAIRsharing.org: ANISEED; Ascidian Network for In Situ Expression and Embryological Data; DOI: https://doi.org/10.25504/FAIRsharing.xp1x9c; Last edited: Sept. 17, 2019, 5:18 p.m.; Last accessed: Jan 03 2022 7:09 p.m.

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phenotype

metasource: Fairsharing.org
version: FAIRsharing.org: ANISEED; Ascidian Network for In Situ Expression and Embryological Data; DOI: https://doi.org/10.25504/FAIRsharing.xp1x9c; Last edited: Sept. 17, 2019, 5:18 p.m.; Last accessed: Jan 03 2022 7:09 p.m.

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genomics databases (non-vertebrate)

metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

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taxonomy and identification

metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

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cell biology

metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:01.032409

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developmental biology

metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:01.032409

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phylogeny

metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:01.032409

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ontology and terminology

metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:01.032409

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data submission, annotation and curation

metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:01.032409

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embryology

metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:01.032409

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biological imaging

metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:01.032409

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animal study

metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:01.032409

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functional genomics

metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:01.032409

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transcriptomics

metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:01.032409

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phylogenomics

metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:01.032409

Close

gene gene expression genome life cycle stage literature curation mutation phenotype genomics taxonomy and identification cell biology developmental biology phylogeny ontology and terminology data submission, annotation and curation embryology biological imaging animal study functional genomics transcriptomics phylogenomics