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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: Sep 3, 2019)

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Resource NameResource TypeDescriptionKeywordsResource IDProper CitationParent OrganizationRelated ConditionFunding AgencyRelationReferenceWebsite StatusAlternate IDsAlternate URLsOld URLs
NIH Knockout Mouse Project (KOMP)Resource, topical portal, portal, data or information resourceA trans-NIH initiative to generate a comprehensive and public resource comprised of mouse embryonic stem (ES) cells containing a null mutation in every gene in the mouse genome. By capitalizing on efficiencies of scale and a centralized production effort, the project intends to make this catalog of mutants available in mouse strain C57BL/6 for two reasons: it is the most widely used strain and it is the strain for which complete genome sequence has been made available. The NIH KOMP initiative aims to: 1) use gene targeting to make the resource of null alleles, marked with a high utility reporter, preferably in C57BL/6; 2) support a repository to house the products of this resource as well as an additional "repatriation" effort to bring into repositories 1000 of the existing high priority mouse knockouts not already stored in a public repository; 3) develop improved C57BL/6 ES cells that show robust germline transmission, so that they may be used in a high throughput pipeline in generating this resource; and 4) implement a data coordination center which will make the status and relevant data of the production effort available to the research community. Towards those ends, NIH awarded five-year cooperative agreements totaling up to $47.2 million to two groups for the creation of the knockout mice lines. Recipients of those awards are Regeneron Pharmaceuticals, Inc., in Tarrytown, N.Y., and a collaborative team from Children's Hospital Oakland Research Institute (CHORI) in Oakland, Calif., the School of Veterinary Medicine, University of California, Davis (UC Davis); and the Wellcome Trust Sanger Institute in Hinxton, England. Under its cooperative agreement, the team plans to systematically create mouse ES cell lines in which 5,000 genes have been knocked out by gene targeting. The VelociGene division of Regeneron, will take aim at a different set of 3,500 genes. Both groups will utilize information from the finished mouse genome sequence to design targeting vectors, which will be built by large-scale, automated technologies. The combined collection of mouse ES cells with knockouts in 8,500 genes will be useful for producing knockout mice. In addition, The Jackson Laboratory will set up a Data Coordination Center that will allow the research community to track the scheduling and progress of knockout production. The center will also serve as a central information resource for all publicly available knockout mutants and will integrate with other databases that contain mouse DNA sequence, additional information on mouse genetics and information on the physical and biochemical characteristics of the knockout mice. The NIH has also provided $4.8 million to establish and support a repository for the Knockout Mouse Project. Finally, NIH awarded cooperative agreements to improve the efficiency of methods for creating knockout lines. They will focus on developing methods to create ES cell lines suitable for high-throughput gene targeting or trapping in C57BL/6.embryonic stem cell, c57bl/6, knock out mouse, gene, mutationSCR_005571(NIH Knockout Mouse Project (KOMP), RRID:SCR_005571)International Knockout Mouse Consortium , National Institutes of Health NIH, NIH Blueprint for Neuroscience Researchrelated to: Monarch Initiative, listed by: NIDDK Information Network, NIDDK Research ResourcesLast checked downnlx_145296
Lifespan Observations DatabaseResource, data or information resource, databaseDatabase that collects published lifespan data across multiple species. The entire database is available for download in various formats including XML, YAML and CSV.lifespan, phenotype, intervention, gene, compound, publicationSCR_001609(Lifespan Observations Database, RRID:SCR_001609)Sageweb Agingrelated to: Monarch Initiative, used by: NIF Data Federation, Aging PortalLast checked downnlx_153873http://sageweb.org/lifespandb
PfamResource, data or information resource, databaseA database of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs). Users can analyze protein sequences for Pfam matches, view Pfam family annotation and alignments, see groups of related families, look at the domain organization of a protein sequence, find the domains on a PDB structure, and query Pfam by keywords. There are two components to Pfam: Pfam-A and Pfam-B. Pfam-A entries are high quality, manually curated families that may automatically generate a supplement using the ADDA database. These automatically generated entries are called Pfam-B. Although of lower quality, Pfam-B families can be useful for identifying functionally conserved regions when no Pfam-A entries are found. Pfam also generates higher-level groupings of related families, known as clans (collections of Pfam-A entries which are related by similarity of sequence, structure or profile-HMM).database, clan, structure, sequence, protein family, domainSCR_004726(Pfam, RRID:SCR_004726)Wellcome Trust Sanger Institute; Hinxton; United Kingdom BBSRC, EMBL core funds, Howard Hughes Medical Institute, Wellcome Trustrelated to: Conserved Domain Database, Monarch Initiative, SUPFAM, DBD: Transcription factor prediction database, DOMINE: Database of Protein Interactions, GeneSpeed- A Database of Unigene Domain Organization , Eukaryotic Linear Motif, TopoSNP, GOTaxExplorer, TrED, ProOpDB, Algal Functional Annotation Tool, used by: Mutation Annotation and Genomic Interpretation, MobiDB, listed by: OMICtoolsReferences (2)Last checked downnlx_72111, OMICS_01696http://pfam.sanger.ac.uk/
MOPED - Model Organism Protein Expression Database Resource, data analysis service, resource, production service resource, analysis service resource, database, service resource, data or information resourceAn expanding multi-omics resource that enables rapid browsing of gene and protein expression information from publicly available studies on humans and model organisms. MOPED also serves the greater research community by enabling users to visualize their own expression data, compare it with existing studies, and share it with others via private accounts. MOPED uniquely provides gene and protein level expression data, meta-analysis capabilities and quantitative data from standardized analysis utilizing SPIRE (Systematic Protein Investigative Research Environment). Data can be queried for specific genes and proteins; browsed based on organism, tissue, localization and condition; and sorted by false discovery rate and expression. MOPED links to various gene, protein, and pathway databases, including GeneCards, Entrez, UniProt, KEGG and Reactome. The current version of MOPED (MOPED 2.5) The current version of MOPED (MOPED 2.5, 2014) contains approximately 5 million total records including ~260 experiments and ~390 conditions.protein expression, gene expression, model organism, gene, protein, pathway, proteomics, transcriptomics, data visualization, overlap plot, heatmap, dot plot, data sharing, protein localization, gene localizationSCR_006065( MOPED - Model Organism Protein Expression Database , RRID:SCR_006065)NIDDK, NIGMS, NSF, Robert B McMillen Foundationrelated to: GeneCards, Universal Protein Resource, KEGG, Reactome, Monarch InitiativeReferences (2)Last checked downnlx_151470
CMHD - Centre for Modeling Human DiseaseResource, database, analysis service resource, production service resource, material service resource, service resource, biomaterial manufacture, data or information resourceMultidisciplinary collaboration undertaking genome-wide mutagenesis to functionally annotate the mouse genome and develop new mouse models relevant to human disease. To achieve these goals two major research platforms are carried out: Gene trapping and ENU Mutagenesis. A new challenge is faced in the post-genomic era - the assignment of biological function to the human genome sequence and projecting that assignment into understanding of human health and disease. The Centre for Modeling Human Disease (CMHD) was established to take part in the worldwide initiative to address these challenges. At the CMHD, two fundamentally different, yet complimentary methods are employed to generate mutant mouse models of human disease: chemical mutagenesis by ethylnitrosourea (ENU), and gene trap insertional mutagenesis. The Centre contributes its resources to similar international efforts and is the first of its kind in Canada. The Center is also actively developing other mutagenic strategies including pharmacologic and genetic modifier screens to dissect disease pathways, and novel mutagenic techniques using embryonic stem cells. ENU Database * Statistics for Mouse Physiological Parameters * Search Mutants by Phenotype * Search Mutants by Heritability Gene Trap Database * Search by in vitro Expression Pattern * Search by Gene Trap Sequences CMHD Members Only (must register and login) * Search Mouse Line * Histopathology * Sperm, Tissue, Slide Archiving * CMHD Database Download CMHD Services * Phenotyping * Genetic Mapping * Pathology * Pathology Service Chargesmutant, mouse model, chemical mutagenesis, ethylnitrosourea, gene trap insertion, mutagenesis, genome-wide mutagenesis, mouse genome, genome, phenotype, heritability, expression pattern, sequence, image, neurobiology, behavior, embryonic stem cell, gene trapping, enu mutagenesis, human diseaseSCR_006101(CMHD - Centre for Modeling Human Disease, RRID:SCR_006101)Toronto Centre for Phenogenomics Human diseaseCIHR, Genome Canadarelated to: Monarch InitiativeLast checked downnlx_151636
Sanger Mouse Resources PortalResource, database, biomaterial supply resource, production service resource, material service resource, service resource, cell repository, material resource, biomaterial manufacture, data or information resourceDatabase of mouse research resources at Sanger: BACs, targeting vectors, targeted ES cells, mutant mouse lines, and phenotypic data generated from the Institute''''s primary screen. The Wellcome Trust Sanger Institute generates, characterizes, and uses a variety of reagents for mouse genetics research. It also aims to facilitate the distribution of these resources to the external scientific community. Here, you will find unified access to the different resources available from the Institute or its collaborators. The resources include: 129S7 and C57BL6/J bacterial artificial chromosomes (BACs), MICER gene targeting vectors, knock-out first conditional-ready gene targeting vectors, embryonic stem (ES) cells with gene targeted mutations or with retroviral gene trap insertions, mutant mouse lines, and phenotypic data generated from the Institute''''s primary screen.bacterial artificial chromosome, vector, embryonic stem cell, mutant mouse line, phenotype, 129s7, c57bl6/j, gene, knockout, gene expression, genetics, chromosome, mutant, mouse line, mammal, marker symbolSCR_006239(Sanger Mouse Resources Portal, RRID:SCR_006239)Wellcome Trust Sanger Institute; Hinxton; United Kingdom European Union, NCRR, NHGRI, Wellcome Trustrelated to: Ensembl, Monarch Initiative, listed by: One Mind Biospecimen Bank ListingLast checked downnlx_151819
Human Genome Variation Society: Databases and Other ToolsResource, data set, data or information resourceA list of various databases freely available to the public, including several mutation and variation resources, such as education resources for teachers students provided by the Human Genome Variation Society. Databases listed include: * Locus Specific Mutation Databases * Disease Centered Central Mutation Databases * Central Mutation and SNP Databases * National and Ethnic Mutation Databases * Mitochondrial Mutation Databases * Chromosomal Variation Databases * Other Mutation Databases ( i.e. your round holes don''''t fit our square pegs) * Clinical and Patient Aspects Databases * Non Human Mutation Databases * Artificial Mutations Only * Other Related Databases * Education Resources for Teachers and Studentsgenome, artificial, chromosome, clinical, disease, human, mitochondrial, non human, snp, mutation, genetic variation, education, ethnicSCR_006876(Human Genome Variation Society: Databases and Other Tools, RRID:SCR_006876)Human Genome Variation Society related to: Monarch InitiativeLast checked downnif-0000-02959
HGVS Locus Specific Mutation DatabasesResource, data or information resource, databaseDatabase of Locus Specific Mutation Databases. Fields include HGNC Gene symbol / OMIM No., Database name / Internet address, and Curators. If you wish to add an LSDB please go to the LSDB Submission Page.mutation, locus, registry, catalog, genome variation, geneSCR_006730(HGVS Locus Specific Mutation Databases, RRID:SCR_006730)Human Genome Variation Society related to: Monarch InitiativeLast checked upnlx_153903
openSNPResource, source code, database, service resource, storage service resource, software resource, data repository, data or information resourceDatabase of raw data from people who have shared their direct-to-customer (DTC) genetic results from 23andMe, deCODEme or FamilyTreeDNA. Logged-In users can search the database for users with specific phenotypes and mass-download all corresponding SNP-datasets. This allows you to get datasets like All genotyping files of openSNP-users that have Alzheimer and the corresponding control group. They are currently working on providing API-access. You can also use JSON to get access to openSNP-data and some other ways: If you want to automate the file-downloads for a given phenotype the RSS-feeds could help you. Inside the RSS-XML there are 2 flags you could use to automatically create correct genotype-groups: gives you the variation of this user at the phenotype you are looking at and gives you the download link. If you were genotyped by 23andMe, deCODEme or FamilyTreeDNA (contact them regarding others) you can upload the raw genotype data which you can download from your DTC test provider. The data will then be openly available for the world to see and download. They also parse these SNPs and annotate them. For annotation they include the manually curated SNPedia and find Open Access primary publications which appear in the journals of The Public Library of Science (PLoS), an Open Access publishing group. Additionally they screen Mendeley, a crowd-sourced repository of scientific publications. You can also publish some of your phenotypes so some day it might get possible to associate some SNPs with phenotypes. You can also share your knowledge about SNPs and phenotypes with other users and can socialize.SNP, genotype, phenotype, snp, genetic variation, disease, trait, genetics, genome wide association study, crowdsourcing, data setSCR_001636(openSNP, RRID:SCR_001636)related to: Monarch InitiativeLast checked upnlx_153904
International Mouse Strain ResourceResource, biomaterial supply resource, material resource, organism supplier, cell repositoryDatabase of mouse strains and stocks available worldwide, that will assist the international research community in finding the mouse resources they need, including inbred, mutant, and genetically engineered mice. The IMSR is a multi-institutional international collaboration supporting the use of the mouse as a model system for studying human biology and disease. The IMSR began with an initial collaboration between the Mouse Genome Informatics (MGI) group at The Jackson Laboratory and the Medical Research Council Mammalian Genetics Unit at Harwell. Additional institutions and collaborators are now contributing mouse resource information to the IMSR. The data content found in the IMSR is as it was supplied by data provider sites. You are encouraged to participate in making this database as complete as possible for all worldwide mouse strain resources. If you or your institution hold mice, cryopreserved gametes or embryos, or ES cell lines that you distribute to other researchers, contributing information about them to the IMSR catalog will make them more widely known.mouse, strain, stock, inbred, mutant, genetically engineered, embryo, embryonic stem cell line, database, knockout mouse, mutant mouse strain, transgenic mouse, embryonic mouse, live mouse, gamete, ovary, sperm, germplasm, model organismSCR_001526(International Mouse Strain Resource, RRID:SCR_001526) MRC Mammalian Genetics Unit , Mouse Genome Informatics (MGI) NLMrelated to: NIF Data Federation, Recombinase (cre) Activity, One Mind Biospecimen Bank Listing, Monarch Initiative, CMMR - Canadian Mouse Mutant Repository, Integrated Cell Lines, used by: BioSample Database at EBI, Integrated Animals, lists: Taconic Biosciences, Oak Ridge Collection at JAX, National Resource Center for Mutant Mice, JAX Mice and Services, National Applied Research Laboratories, Oriental BioService Inc.References (2)Last checked upnif-0000-09876
PhenoGen InformaticsResource, source code, data analysis service, production service resource, analysis service resource, data set, service resource, storage service resource, software resource, data repository, data or information resourceA toolbox for storing, analyzing and integrating microarray data and related genotype and phenotype data. The site is particularly suited for combining QTL and microarray data to search for candidate genes contributing to complex traits. In addition, the site allows, if desired by the investigators, sharing of the data. Investigators can conduct in-silico microarray experiments using their own and/or shared data. There are five major sections of the site: Genome/Transcriptome Data Browser, Microarray Analysis Tools, Gene List Analysis Tools, QTL Tools, and Downloads. The genome/transcriptome data browser combines a genome browser with all the microarray, RNA-Seq, and Genomic Sequencing data. This provides an effective platform to view all of this data side by side. Source code is available on GitHub.genome, transcription, microarray, gene, quantitative trait loci, analysis, complex trait, genotype, phenotype, high-throughput, rna-seq, snp, genomic marker, region, data sharing, normalize, statistics, gene list, pathway, expression value, expression, correlation, exon, annotation, promoter, homolog, brain, heart, liver, adipose, candidate gene, genetics, transcriptome, eqtl, genome browser, inbred panelSCR_001613(PhenoGen Informatics, RRID:SCR_001613)University of Colorado Denver; Colorado; USA NIAAArelated to: Monarch InitiativePMID:17760997Last checked upnlx_153879, rid_000093http://phenogen.uchsc.edu
Expression Patterns for C. elegans promoter GFP fusionsResource, data set, data or information resource, databaseDatabase of expression patterns of C. elegans promoter - GFP constructs. A text description of the observed pattern is provided, indicating the stage(s) and tissue(s) in which GFP is expressed. Also available for some strains are the corresponding 2D and 3D images. Investigators may browse the entire list, search by gene name, tissue, stage, and pattern. Search results may be downloaded in .csv and .txt formats. Monitoring in vivo expression of the fusion constucts in transgenic worms allows the determination of the developmental stage, tissue, and in some cases, the cells where a particular gene is expressed. Their goal was to build promoter GFP fusion constructs for C. elegans genes that have human orthologues. Of the over 5000 genes that fall into this category, promoter fusion constructs were created for 2000 of these, with a focus on genes expressed in muscle and nerve tissues. When coupled with SAGE and knockout data, this provides valuable and more complete expression profiles for cells, tissues, and developmental stages. A number of strains in which GFP expression was not detected, or expression was lost before the strain could be fully analyzed has been compiled from the project. There are a number of possible causes. A listing Genes without GFP expression is provided and merely useful as a comparison baseline for other projects when they use these promoter regions. No conclusions can be drawn from this data. They are in the process of sending stable strains to the CGC, however there are a limited number of strains available at the moment. The strains that are not available through the CGC may be requested through Rebecca Newbury. The images posted on the website are also available by request.gene expression, expression pattern, tissue, green fluorescent protein, image, image collection, development, embryo, adult, ortholog, human ortholog, gene, video, stage of development, locus, genomic location, transgene, mutagen, organism supplier, cell, developmental stage, in vivoSCR_001619(Expression Patterns for C. elegans promoter GFP fusions, RRID:SCR_001619)Albert Einstein College of Medicine; New York; USA Genome British Columbia, Genome Canadarelated to: WormAtlas: A Database of Behavioral and Structural Anatomy of C. elegans, WormBase, Caenorhabditis Genetics Center, Monarch Initiative, listed by: One Mind Biospecimen Bank ListingPMID:17850180Last checked upnlx_153885
Human Gene Mutation DatabaseResource, data or information resource, databaseCurated database of known (published) gene lesions responsible for human inherited disease.gene, disease, gene lesion, mutation, deletion, insertion, duplication, rearrangement, nuclear gene, functional polymorphismSCR_001621(Human Gene Mutation Database, RRID:SCR_001621)Cardiff University; Wales; United Kingdom Inherited diseaserelated to: BIOBASE Corporation, Monarch Initiative, listed by: OMICtoolsReferences (11)Last checked upnlx_153887, OMICS_00281http://www.hgmd.cf.ac.uk/ac/index.php
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
AnimalTFDBResource, data or information resource, databaseA comprehensive transcription factor (TF) database in which they identified and classified all the genome-wide TFs in 50 sequenced animal genomes (Ensembl release version 60). In addition to TFs, it also collects transcription co-factors and chromatin remodeling factors of those genomes, which play regulatory roles in transcription. Here they defined the TFs as proteins containing a sequence-specific DNA-binding domain (DBD) and regulating target gene expression. Currently, the AnimalTFDB classifies all the animal TFs into 72 families according to their conserved DBDs. Gene lists of transcription factors, transcription co-factors and chromatin remodeling factors of each species are available for downloading.transcription factor, dna-binding domain, transcription co-factor, chromatin remodeling factor, gene structure, functional domain, go annotation, protein interaction, ortholog, paralog, 3d structure, pathway, protein-protein interaction, binding site, target, data set, image collection, 3d spatial imageSCR_001624(AnimalTFDB, RRID:SCR_001624)Huazhong University of Science and Technology; Wuhan; China Fundamental Research Funds for the Central Universities, Huazhong University of Science and Technology; Wuhan; China, National Natural Science Foundation of Chinarelated to: Gene Ontology, Ensembl, Monarch Initiative, listed by: OMICtoolsPMID:22080564Last checked upnlx_153892, OMICS_01856
MouseCycResource, data analysis service, production service resource, analysis service resource, database, service resource, data or information resourceA manually curated database of both known and predicted metabolic pathways for the laboratory mouse. It has been integrated with genetic and genomic data for the laboratory mouse available from the Mouse Genome Informatics database and with pathway data from other organisms, including human. The database records for 1,060 genes in Mouse Genome Informatics (MGI) are linked directly to 294 pathways with 1,790 compounds and 1,122 enzymatic reactions in MouseCyc. (Aug. 2013) BLAST and other tools are available. The initial focus for the development of MouseCyc is on metabolism and includes such cell level processes as biosynthesis, degradation, energy production, and detoxification. MouseCyc differs from existing pathway databases and software tools because of the extent to which the pathway information in MouseCyc is integrated with the wealth of biological knowledge for the laboratory mouse that is available from the Mouse Genome Informatics (MGI) database.energy production, biosynthesis, cell, cellular, degradation, detoxification, metabolism, mouse, physiological, enzymatic reaction, gene, disease, genome, metabolic pathway, pathway, compound, enzymatic reaction, protein, rna, reaction, blast, human, mammal, genetic, genomicSCR_001791(MouseCyc, RRID:SCR_001791)Jackson Laboratory NHGRIrelated to: Mouse Genome Informatics (MGI), Gene Ontology, Monarch InitiativePMID:19682380Last checked upnif-0000-10303
PhosphoSitePlus: Protein Modification SiteResource, knowledge environment resource, portal, data or information resourceA freely accessible on-line systems biology resource devoted to all aspects of protein modification, as well as other post-translational modifications. It provides valuable and unique tools for both cell biologists and mass spectroscopists. PhosphoSite is a human- and mouse-centric database. It includes features such as: viewing the locations of modified residues on molecular models; browsing and searching MS2 records by disease, tissue, and cell line; submitting lists of peptides to identify previously reported genes; searching by sub-cellular localization, treatment, tissues, cell types, cell lines and diseases, and protein types and protein domains; searching for experimentally-verified kinase substrates and viewing preferred substrate motifs; and viewing MS2 spectra for peptides and sites not previously published.portal, mass spectroscopist, molecular model, mouse, post translational, subcellular localization, protein modification, post-translational modification, protein phosphorylation, protein structure, protein function, ubiquitinylation, acetylation, cellular component, cell type, visualization, data repositorySCR_001837(PhosphoSitePlus: Protein Modification Site, RRID:SCR_001837)Cell Signaling Technology NCI, NIAAA, NIGMSrelated to: Cytoscape, Monarch Initiative, ConsensusPathDBPMID:22135298Last checked upnif-0000-10399
Bgee: a dataBase for Gene Expression EvolutionResource, data or information resource, databaseDatabase to retrieve and compare gene expression patterns between animal species. Bgee first maps heterogeneous expression data (currently RNA-Seq, Affymetrix, in situ hybridization, and EST data) to anatomy and development of different species.gene expression, rna-seq, affymetrix, in situ hybridization, expressed sequence tag, cross specie, comparison, homology, anatomy, developmental stage, gene expression pattern, development, genome, function, chordate, fish, transcriptiome, embryo, adult, mirna, protein coding, prenatal, immature, post-embryonic development, alimentary system, cardiovascular system, nervous system, renal system, reproductive system, respiratory system, skeletal system, ortholog, ontologySCR_002028(Bgee: a dataBase for Gene Expression Evolution, RRID:SCR_002028)SIB Swiss Institute of Bioinformatics related to: Gene Expression Omnibus, NCBI Sequence Read Archive, ArrayExpress, Zebra Model Organism Database (ZFIN), Xenbase, Mouse Genome Informatics (MGI), Berkeley Drosophila Genome Project, UniGene, Zebrafish Anatomical Ontology, eVOC, Adult Mouse Anatomy Ontology, Xenopus Anatomy Ontology, Drosophila anatomy and development ontologies, Ensembl, Monarch InitiativeLast checked upnif-0000-11819
Mouse Neuronal Expression DatabaseResource, data or information resource, databaseDatabase of microarray analysis of twelve major classes of fluorescent labeled neurons within the adult mouse forebrain that provide the first comprehensive view of gene expression differences. The publicly available datasets demonstrate a profound molecular heterogeneity among neuronal subtypes, represented disproportionately by gene paralogs, and begin to reveal the genetic programs underlying the fundamental divisions between neuronal classes including that between glutamatergic and GABAergic neurons. Five of the 12 populations were chosen from cingulate cortex and included several subtypes of GABAergic interneurons and pyramidal neurons. The remaining seven were derived from the somatosensory cortex, hippocampus, amygdala and thalamus. Using these expression profiles, they were able to construct a taxonomic tree that reflected the expected major relationships between these populations, such as the distinction between cortical interneurons and projection neurons. The taxonomic tree indicated highly heterogeneous gene expression even within a single region. This dataset should be useful for the classification of unknown neuronal subtypes, the investigation of specifically expressed genes and the genetic manipulation of specific neuronal circuit elements. Datasets: * Full: Here you can query gene expression results for the neuronal populations * Strain: Here you can query the same expression results accessed under the full checkbox, with one additional population (CT6-CG2) included as a control for the effects of mouse strain. This population is identical to CT6-CG (YFPH) except the neurons were derived from wild-type mice of three distinct strains: G42, G30, and GIN. * Arlotta: Here you can query the same expression results accessed under the full checkbox, with nine additional populations from the dataset of Arlotta et al., 2005. These populations were purified by FACS after retrograde labeling with fluorescent microspheres. Populations are designated by the prefix ACS for corticospinal neurons, ACC for corticocallosal neurons and ACT for corticotectal neurons, followed by the suffix E18 for gestational age 18 embryos, or P3, P6 and P14 for postnatal day 3, 6 and 14 pups. For each successful gene query the following information is returned: # Signal level line plot: Signal level is plotted on Y-axis (log base 2) for each sample. Samples include the thirty six representing the twelve populations profiled in Sugino et al. In addition, six samples from homogenized (=dissociated and but not sorted) cortex are included representing two different strains: G42-HO is homogenate from strain G42, GIN-HO is homogenate from stain GIN. # Signal level raster plots: Signal level is represented by color (dark red is low, bright red is high) for all samples. Color scale is set to match minimum (dark red) and maximum (bright yellow) signal levels within the displayed set of probe sets. # Scaled signal level raster plots: Same as 2) except color scale is adjusted separately for each gene according to its maximum and minimum signal level. # Table: Basic information about the returned probe sets: * Affymetrix affyid of probe set * NCBI gene symbol, NCBI gene name * NCBI geneID * P-value score from ANOVA for each gene is also given if available (_anv column). P-value represents the probability that there is no difference in the expression across cell types.expression profile, forebrain, functional, gabaergic neuron, amygdala, array, cell type, cell type comparison, microarray, cingulate cortex, classify, genomics, glutamatergic, hippocampus, interneuron, molecular, adult mouse, neuron, pyramidal neuron, somatosensory cortex, taxonomy, thalamus, gene, embryonic mouseSCR_002043(Mouse Neuronal Expression Database, RRID:SCR_002043)CRE Driver Network related to: Monarch InitiativeLast checked upnif-0000-12084http://mouse.bio.brandeis.edu:8080/
Rat Resource and Research CenterResource, organism supplier, biomaterial supply resource, biospecimen repository, tissue bank, service resource, storage service resource, cell repository, material resource, material storage repositoryCenter that supplies biomedical investigators with the rat models, embryonic stem cells, related reagents, and the protocols they require for their research. In addition to repository, cryostorage and distribution functions, the RRRC can facilitate acquisition of rat strains from other international repositories as well as provide consultation and technical training to investigators using rat models.embryo, gamete, animal, drug, biomedical, cryopreserved, disease, genome, genotyping, germplasma, human, hybrid, inbred, infectious, molecular, mutant, nuclear, ovarian, pathogen, rat, research, tissue, rat model, embryonic stem cell, reagent, protocol, cell line, stem cell, strain, database, catalogSCR_002044(Rat Resource and Research Center, RRID:SCR_002044)University of Missouri; Missouri; USA NCRR, NIH Office of the Directorrelated to: One Mind Biospecimen Bank Listing, Monarch Initiative, listed by: One Mind Biospecimen Bank ListingLast checked upnif-0000-12085http://www.nrrrc.missouri.edu/
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