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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.

(last updated: Aug 10, 2019)

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Resource NameResource TypeDescriptionKeywordsResource IDProper CitationParent OrganizationRelated ConditionFunding AgencyRelationReferenceWebsite StatusAlternate IDsAlternate URLsOld URLs
FishFace - An atlas of zebrafish craniofacial developmentResource, atlas, reference atlas, data or information resourceishFace is an atlas of zebrafish craniofacial development. How do the elements of the craniofacial skeleton arise, grow, and reshape? Answers to this question are coming from both molecular-genetic and cell-biological approaches, which rely, first of all, on precise description of the developmental events and processes that comprise skeletogenesis. Zebrafish, with a sophisticated knowledge of its genetics and genomics, with favorable attributes for phenotypic analyses of development, and with patterns of development conserved among all vertebrates, provides a powerful animal model for learning about craniofacial development. In particular, with current transgenic approaches one can examine craniofacial skeletal elements in exquisite cellular detail during an extended period of development within living, intact embryos and larvae an investigative method unsurpassed in accuracy and sensitivity. We constructed this developmental atlas of the craniofacial skeleton, FishFace, to serve as a guide for such study. We hope that the FishFace Atlas will be particularly useful in comparative and mutational analyses where there is interest in understanding the cellular basis of early skeletogenesis. The heart of the FishFace Atlas uses high magnification (generally a 40x objective) confocal image stacks showing transgenically-labelled chondrocytes or osteoblasts, along with mineralized bone matrix, which is visualized by vital staining with Alizarin red. We present these stacks in sequences that follow particular individual cartilages and bones of the first two pharyngeal arches as they develop during embryonic and larval stages. To do so, we build on the foundation set out in the gold standard reference for describing comprehensively skeletal elements in the zebrafish craniofacial complex, Cubbage and Mabee (1996), which used fixed preparations stained for cartilage and bone through adult stages. The FishFace Atlas element development section adds considerable detail to arch one and two early development, particularly at the cellular level, but also in description of element growth and shaping. Other sections of the FishFace Atlas, at lower magnification, provide anatomical context for the element development section, including an interactive tool made by optical projection tomography (OPT) for learning the anatomy of the entire larval skull. Hence, the FishFace Atlas provides the community with an interactive resource with which the user can understand not only the cellular details, but also complex 3D anatomical relationships, of developing elements in the craniofacial skeleton of the zebrafish.craniofacial developmentSCR_008894(FishFace - An atlas of zebrafish craniofacial development, RRID:SCR_008894)FaceBase ARRA, NICHD, NIDCRLast checked upnlx_151378
Zebrafish RNAi DatabaseResource, topical portal, organism-related portal, service resource, portal, storage service resource, data repository, data or information resourceCommunity built zebrafish RNAi platform that contains plasmids, successfully targeted genes and shRNA sequences, and a forum for discussion. This is a true community platform with users who add data, modify entiries, request features and share using the discussion board.plasmid, gene, shrna sequence, rnai, methodSCR_008965(Zebrafish RNAi Database, RRID:SCR_008965)Massachusetts Institute of Technology; Massachusetts; USA Last checked downnlx_152032
Zebrafish Neuroscience Research ConsortiumResource, group, training resourceA group of scientists who collaborate and promote zebrafish neuroscience research. The consortium has opportunities for networking, scholarly publications and zebrafish-related symposia and conferences. The consortium is a supporter of the Zebrafish Neurophenome Project (ZNP), an initiative for a database of zebrafish behavioral and physiological data in an online, open source format.zebrafish, consortium, research, publication, scholar, neuroscience, behavioral activitySCR_000298(Zebrafish Neuroscience Research Consortium, RRID:SCR_000298)Last checked upnlx_151974
ARNIEResource, data analysis service, production service resource, analysis service resource, database, service resource, data or information resourceDatabase that integrates the extracellular protein interaction network generated in our lab using AVEXIS technology with spatiotemporal expression patterns for all genes in the network. The tool allows users to browse the network by clicking on individual proteins, or by specifying the spatiotemporal parameters. Clicking on connector lines will allow users to compare stage-matched expression patterns for genes encoding interacting proteins. Additionally, users can rapidly search for their genes in the network using the BLAST server provided.network, orthologue, paralogue, gene, orthologue, protein interaction, protein, blast, extracellular, expression profiling, interaction network, ligand, interaction, signalingSCR_000514(ARNIE, RRID:SCR_000514)Wellcome Trust Sanger Institute; Hinxton; United Kingdom MRC, Wellcome Trustlisted by: OMICtoolsPMID:20802085Last checked upOMICS_01529
Zebrafish Brain AtlasResource, reference atlas, service resource, storage service resource, atlas, image repository, data repository, data or information resourceCollates and curates neuroanatomical data and information generated both in-house and by the community to communicate the current state of knowledge about neuroanatomical structures in the developing zebrafish. Most of the data will come from high resolution confocal imaging of intact brains in which neuroanatomical structures are labelled by combinations of transgenes and antibodies. The intention is to make the data intuitively accessible to all: not just those with expertise in neuroanatomy. Zebrafishbrain.org is intended to be a community repository for image-based data related to the neuroanatomy of the zebrafish. They encourage users to participate though the uploading and annotation of data and the writing of tutorials on structures. Please contact them if you would like to contribute. During the course of the project they have used around 40 different transgenic lines for imaging. These lines are all maintained in their facility. All of these lines are or have been freely available for distribution to the community. Please contact them to arrange this.brain, neuroanatomy, developing, transgene, antibody, confocal, section, reconstruction, high-resolution, developmental stage, embryo, brain structure, confocal imaging, comparative anatomy, transgenic, 3d spatial image, video, embryonic zebrafish, development, annotation, narrative resource, training material, cell repositorySCR_000606(Zebrafish Brain Atlas, RRID:SCR_000606)University College London; London; United Kingdom BBSRC, European Union, Wellcome Trustrecommends: Zebrafish Anatomical Ontology, listed by: One Mind Biospecimen Bank ListingLast checked upnlx_149455
Wnt homepageResource, topical portal, portal, data or information resourceA resource for members of the Wnt community, providing information on progress in the field, maps on signaling pathways, and methods. The page on reagents lists many resources generously made available to and by the Wnt community. Wnt signaling is discussed in many reviews and in a recent book. There are usually several Wnt meetings per year.wnt signaling, wnt, wnt protein, wnt pathway, signaling, pathway, method, protein, reagent, bibliographySCR_000662(Wnt homepage, RRID:SCR_000662)Stanford University; Stanford; California CancerLast checked upnlx_156863
Disease Genes Conserved Sequence Tags DatabaseResource, data or information resource, databaseA database of conserved sequence elements, identified by a systematic genomic sequence comparison between a set of human genes involved in the pathogenesis of genetic disorders and their murine counterparts. Human and mouse genomic sequences were compared by BLASTZ. Sequences longer than 100 and with identity better than 70 were selected as CSTs and imported into the database. CSTs are extensively annotated with respect to exon/intron structure and other biological parameters. CST counterparts in other species were identified by using BLAST to scan genomes from other species, and selecting on the basis of homology and co-linearity. The database can be accessed by gene, chromosomal location, graphic browser, DNA features, and coding regions.database, conserved sequence element, genomic sequence, human gene, pathogenesis, genetic disorder, blastz, cstSCR_000760(Disease Genes Conserved Sequence Tags Database, RRID:SCR_000760)BioGeM, Regione Campania, Telethon Foundation, the Associazione Italiana per la Ricerca sul Cancro (AIRC), the Federazione Italiana per la Ricerca sul Cancro (FIRC), the Italian Ministry for Research (MURST), the National Council for Research (CNR)DOI:10.1093/nar/gki011Last checked upnif-0000-21121
ZCreResource, biomaterial supply resource, material resourceZCre is a consortium of researchers who have a shared interest in developing Cre/lox based tools for use in the zebrafish model organism. ZCre plans to generate 15 or more tissue specific ERT2CreERT2 driver lines to be expressed in either differentiated cell types or precursor/stem cells, as well as 20 or more lines based upon multilox technology. One set of multilox transgenes will allow long-term permanent labelling of individual cells for lineage tracing and other applications. Another set will allow perturbation of single pathways within individual cells (PathM lines). In order to make these lines ZCre has developed a three-way cloning system using Gateway technology (Invitrogen). Once constructs are made they will be deposited at Addgene.org. Transgenic lines will be available from ZCre or from regional stock centers as requested.cre, clone, cre transgenic line, lox transgenic line, ert2creert2 driver line, transgenic line, constructSCR_000815(ZCre, RRID:SCR_000815)University of Sheffield; South Yorkshire; United Kingdom , University of Bath; North East Somerset; United Kingdom Medical Research Council UKuses: Addgene, listed by: One Mind Biospecimen Bank ListingLast checked upnlx_151618
Zebrafish - SCORE Imaging: Specimen in a Corrected Optical Rotational EnclosureResource, narrative resource, data or information resourceNarrative resource describing a visual data analysis and collection approach that takes advantage of the cylindrical nature of the zebrafish allowing for an efficient and effective method for image capture called, Specimen in a Corrected Optical Rotational Enclosure (SCORE) Imaging. To achieve a non-distorted image, zebrafish were placed in a fluorinated ethylene propylene (FEP) tube with a surrounding, optically corrected imaging solution: water. By similarly matching the refractive index of the housing (FEP tubing) to that of the inner liquid and outer liquid (water), distortion was markedly reduced, producing a crisp imagable specimen that is able to be fully rotated 360 degrees. A similar procedure was established for fixed zebrafish embryos using convenient, readily available borosilicate capillaries surrounded by 75% glycerol. The method described could be applied to chemical genetic screening and other, related high-throughput methods within the fish community and among other scientific fields.format, authoring tool, embryo, microscopy, publishing format, imageSCR_001300(Zebrafish - SCORE Imaging: Specimen in a Corrected Optical Rotational Enclosure, RRID:SCR_001300)Mayo Clinic Minnesota; Minnesota; USA , University of Minnesota Twin Cities; Minnesota; USA NIDA, NIGMSlisted by: FORCE11PMID:20528262Last checked upnif-0000-07749
Teleost Anatomy OntologyResource, ontology, data or information resource, controlled vocabularyA multi-species anatomy ontology for teleost fishes. It was originally seeded from ZFA, but covers terms relevant to other taxa. The TAO uses terms from the Common Anatomy Reference Ontology (CARO) as a template for its upper level nodes, and the Vertebrate Skeletal Anatomy Ontology (VSAO) for general skeletal anatomy classes. Growth of the TAO is enabled by contributions from data curators and the ichthyological community. The TAO can be browsed by using the NCBO BioPortal and data annotated using TAO terms can be queried using the Phenoscape Knowedgebase.homology, anatomy, morphology, fish, obo, organismal, zebrafish anatomySCR_001610(Teleost Anatomy Ontology, RRID:SCR_001610)Phenoscape used by: Phenoscape Knowledgebase, uses: Zebrafish Anatomical Ontology, Common Anatomy Reference Ontology, Vertebrate Skeletal Anatomy Ontology, listed by: BioPortal, OBOPMID:20547776Last checked upnlx_153876http://purl.obolibrary.org/obo/tao.obo, http://bioportal.bioontology.org/ontologies/38362?p=termshttps://www.nescent.org/phenoscape/
AncoraResource, data analysis service, production service resource, analysis service resource, database, service resource, data or information resourceWeb resource that provides data and tools for exploring genomic organization of highly conserved noncoding elements (HCNEs) for multiple genomes. It includes a genome browser that shows HCNE locations and features novel HCNE density plots as a powerful tool to discover developmental regulatory genes and distinguish their regulatory elements and domains. They identify HCNEs as non-exonic regions of high similarity between genome sequences from distantly related organisms, such as human and fish, and provide tools for studying the distribution of HCNEs along chromosomes. Major peaks of HCNE density along chromosomes most often coincide with developmental regulatory genes. Their aim with this site is to aid discovery of developmental regulatory genes, their regulatory domains and their fundamental regulatory elements.genome, highly conserved noncoding element, noncoding element, regulatory gene, regulatory domain, regulatory element, developmental regulatory gene, evolution, enhancerSCR_001623(Ancora, RRID:SCR_001623)University of Bergen; Bergen; Norway Bergen Research Foundation, Research Council of Norway, Sars Centrerelated to: Monarch InitiativePMID:18279518Last checked upnlx_153891
Cold Spring Harbor Protocols: Collected Resources - Behavioral AssaysResource, bibliography, data or information resourceA bibliography of published Behavioral Assays by Cold Spring Harbor Protocols. Cold Spring Harbor Protocols is an interdisciplinary journal providing a definitive source of research methods in cell, developmental and molecular biology, genetics, bioinformatics, protein science, computational biology, immunology, neuroscience and imaging. Each monthly issue details multiple essential methods - a mix of cutting-edge and well-established techniques. Newly commissioned protocols and unsolicited submissions are supplemented with articles based on Cold Spring Harbor Laboratorys renowned courses and manuals. All protocols are up-to-date and presented in a consistent, easy-to-follow format.genetics, bioinformatics, cell, computational biology, development, imaging, immunology, journal, molecular, neuroscience, protein, research, behavioral assay, behavior, ant, honeybee, learning, courtship, larvae, adult, stress, olfactory, aggression, sleep, movement, locomotor, circadian, feedingSCR_001697(Cold Spring Harbor Protocols: Collected Resources - Behavioral Assays, RRID:SCR_001697)Cold Spring Harbor Laboratory Last checked upnif-0000-10198
RAVENResource, data analysis service, production service resource, analysis service resource, database, service resource, data or information resourceTool to search for putative regulatory genetic variation in your favorite gene. Single nucleotide polymorphisms (SNPs) (from dbSNP and user defined) are analyzed for overlap with potential transcription factor binding sites (TFBS) and phylogenetic footprinting using UCSC phastCons scores from multiple alignments of 8 vertebrate genomes.transcription factor binding site, phylogenetic footprint, regulatory sequence variation, genetic variation, in silico, regulatory sequenceSCR_001937(RAVEN, RRID:SCR_001937)University of British Columbia; British Columbia; Canada uses: Embassy-domsearch, listed by: OMICtoolsPMID:18208319Last checked downOMICS_01932
Zebrafish Information ServerResource, topical portal, data or information resource, portal, organism-related portalA portal to different zebrafish resources such as jobs, book, journals, database, meetings, and K-12 programs. Most information leads to ZFIN: The Zebrafish Model Organism Database.database, job, k12 program, journal, monitor, zebrafish, book, meeting, methodSCR_002237(Zebrafish Information Server, RRID:SCR_002237)University of South Carolina; South Carolina; USA Last checked upnif-0000-21003
EnsemblResource, data analysis service, data access protocol, database, web service, production service resource, analysis service resource, catalog, service resource, software resource, data or information resourceCollection of genome databases for vertebrates and other eukaryotic species with DNA and protein sequence search capabilities. Used to automatically annotate genome, integrate this annotation with other available biological data and make data publicly available via web. Ensembl tools include BLAST, BLAT, BioMart and the Variant Effect Predictor (VEP) for all supported species.collection, genome, dataset, database, vertebrate, eukaryotic, DNA, protein, sequence, search, automaticly, annotate, dataSCR_002344(Ensembl, RRID:SCR_002344)European Bioinformatics Institute , Wellcome Trust Sanger Institute; Hinxton; United Kingdom BBSRC, EMBL, European Union, FP6, FP7, MRC, NHGRI, Wellcome Trustrelated to: Ensembl Genomes, GermOnline, CandiSNPer, Human Splicing Finder, NGS-SNP, Sanger Mouse Resources Portal, DECIPHER, Ensembl Genomes, PeptideAtlas, AnimalTFDB, Bgee: a dataBase for Gene Expression Evolution, FlyMine, Rat Gene Symbol Tracker, UniParc at the EBI, go-db-perl, UniParc, G:Profiler, RIKEN integrated database of mammals, VBASE2, p300db, used by: NIF Data Federation, Animal QTLdb, Monarch Initiative, ChannelPedia, Blueprint Epigenome, HmtPhenome, listed by: OMICtools, Biositemaps, re3data.org, LabWorm, works_with: Genotate, CellPhoneDBReferences (2)Last checked upnif-0000-21145, OMICS_01647
Eukaryotic Promoter DatabaseResource, data or information resource, databaseDatabase for an annotated non-redundant collection of eukaryotic POL II promoters, for which the transcription start site has been determined experimentally. Access to promoter sequences is provided by pointers to positions in nucleotide sequence entries. The annotation part of an entry includes description of the initiation site mapping data, cross-references to other databases, and bibliographic references. EPD is structured in a way that facilitates dynamic extraction of biologically meaningful promoter subsets for comparative sequence analysis.promoter, polymerase, polymerase ii, promoter sequence, transcription start site, high-throughput, cage, oligocapping, chip-seq, h2az, h3k4me3, pol-ii, dna methylationSCR_002485(Eukaryotic Promoter Database, RRID:SCR_002485)SIB Swiss Institute of Bioinformatics listed by: OMICtoolsPMID:14681364Last checked upnif-0000-02806, OMICS_01880http://epd.vital-it.ch/
GlimmerHMMResource, software resource, source codeA gene finder based on a Generalized Hidden Markov Model (GHMM). Although the gene finder conforms to the overall mathematical framework of a GHMM, additionally it incorporates splice site models adapted from the GeneSplicer program and a decision tree adapted from GlimmerM. It also utilizes Interpolated Markov Models for the coding and noncoding models . Currently, GlimmerHMM's GHMM structure includes introns of each phase, intergenic regions, and four types of exons (initial, internal, final, and single).gene, hidden markov modelSCR_002654(GlimmerHMM, RRID:SCR_002654)Johns Hopkins University; Maryland; USA NIH, NLMrelated to: GlimmerPMID:15145805Last checked upnlx_156092
GermOnlineResource, data or information resource, databaseCross-species microarray expression database focusing on high-throughput expression data relevant for germline development, meiosis and gametogenesis as well as the mitotic cell cycle. The database contains a unique combination of information: 1) High-throughput expression data obtained with whole-genome high-density oligonucleotide microarrays (GeneChips). 2) Sample annotation (mouse over the sample name and click on it) using the Multiomics Information Management and Annotation System (MIMAS 3.0). 3) In vivo protein-DNA binding data and protein-protein interaction data (available for selected species). 4) Genome annotation information from Ensembl version 50. 5) Orthologs are identified using data from Ensembl and OMA and linked to each other via a section in the report pages. The portal provides access to the Saccharomyces Genomics Viewer (SGV) which facilitates online interpretation of complex data from experiments with high-density oligonucleotide tiling microarrays that cover the entire yeast genome. The database displays only expression data obtained with high-density oligonucleotide microarrays (GeneChips).fertility, development, germline, microarray, annotation, in vivo, protein-dna binding, protein-protein interaction, genome, ortholog, high-density oligonucleotide microarray, gene expression, genome annotation, gene orthology, genechip, tiling array, development, meiosis, gametogenesis, mitotic cell cycle, data set, data repositorySCR_002807(GermOnline, RRID:SCR_002807)National Institute of Health and Medical Research; Rennes; France bioinformatics platform of Biogenouest, National Institute of Health and Medical Research; Rennes; France, Swiss Institute of Bioinformatics, University of Rennes 1; Rennes; Francerelated to: Ensembl, OMA Browser, listed by: 3DVC, re3data.orgPMID:21149299Last checked upnif-0000-02906
MapViewerResource, data or information resource, databaseDatabase that provides special browsing capabilities for a subset of organisms in Entrez Genomes. Map Viewer allows users to view and search an organism's complete genome, display chromosome maps, and zoom into progressively greater levels of detail, down to the sequence data for a region of interest. If multiple maps are available for a chromosome, it displays them aligned to each other based on shared marker and gene names, and, for the sequence maps, based on a common sequence coordinate system.genome, mapping, sequencing, chromosomeSCR_003092(MapViewer, RRID:SCR_003092)NCBI related to: NCBI Genome, Consensus CDS, listed by: OMICtoolsLast checked upnif-0000-03103, OMICS_00921
miRNAMapResource, data or information resource, databaseA database of experimentally verified microRNAs and miRNA target genes in human, mouse, rat, and other metazoan genomes. In addition to known miRNA targets, three computational tools previously developed, such as miRanda, RNAhybrid and TargetScan, were applied for identifying miRNA targets in 3'-UTR of genes. In order to reduce the false positive prediction of miRNA targets, several criteria are supported for filtering the putative miRNA targets. Furthermore, miRNA expression profiles can provide valuable clues for investigating the properties of miRNAs, such tissue specificity and differential expression in cancer/normal cell. Therefore, we performed the Q-PCR experiments for monitoring the expression profiles of 224 human miRNAs in eighteen major normal tissues in human. The cross-reference between the miRNA expression profiles and the expression profiles of its target genes can provide effective viewpoint to understand the regulatory functions of the miRNA.microrna, genomeSCR_003156(miRNAMap, RRID:SCR_003156)National Chiao Tung University; Hsinchu; Taiwan listed by: OMICtoolsReferences (2)Last checked upnif-0000-03138, OMICS_00408
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