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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Rodent Brain WorkBench Resource Report Resource Website 10+ mentions |
Rodent Brain WorkBench (RRID:SCR_002727) | rbwb | atlas, data or information resource, data processing software, data visualization software, database, software application, software resource | The Rodent Brain WorkBench is the portal to atlases, databases and tools developed by the Neural Systems and Graphics Computing Laboratory (NeSys) at the Centre for Molecular Biology and Neuroscience (CMBN), University of Oslo, Oslo, Norway. The Rodent Brain WorkBench presents a collection of brain mapping and atlasing oriented database applications and tools. The main category of available data is high resolution mosaic images covering complete histological sections through the rat and mouse brain. A highly structured relational database system for archiving, retrieving, viewing, and analysing microscopy and imaging data, aiming at presentation in standardized brain atlas space, is used to present a series of web applications for individual research projects. * Brain Connectivity * Atlases of Mouse Brain Promoter Gene Expression * General Brain Atlas and Navigation Systems * Downloadable tools for 3-DVisualization Open Access: * Atlas 3D * Cerebro-Cerebellar I * Cerebro-Cerebellar II * Neurotransporter Atlas * Rat Hippocampus * Tet-Off Atlas I (PrP) * Tet-Off Atlas II (PrP/CamKII) * Whole Brain Connectivity Atlas The data presented have been produced in collaboration with a large number of laboratories in Europe and the United States. | electron microscopy, image, brain, cerebellar cortex, hippocampus, connectivity, coronal section, high resolution, light microscopy, histology, microscopy, mouse brain, mouse brain atlas, mpeg, mri, nerve cell, nifti, neuroimaging, rat, rat brain, rodent brain, stereotaxic coordinate, xyz coordinate, gene expression | has parent organization: University of Oslo; Oslo; Norway | Free, Freely available | nif-0000-00424 | SCR_002727 | Rodent Brain Work Bench | 2026-09-05 06:24:52 | 21 | |||||||
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SumsDB Resource Report Resource Website 10+ mentions |
SumsDB (RRID:SCR_002759) | SumsDB, WebCaret | analysis service resource, atlas, data analysis service, data or information resource, data repository, database, image repository, production service resource, service resource, storage service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on May 11, 2016. Repository of brain-mapping data (surfaces and volumes; structural and functional data) derived from studies including fMRI and MRI from many laboratories, providing convenient access to a growing body of neuroimaging and related data. WebCaret is an online visualization tool for viewing SumsDB datasets. SumsDB includes: * data on cerebral cortex and cerebellar cortex * individual subject data and population data mapped to atlases * data from FreeSurfer and other brainmapping software besides Caret SumsDB provides multiple levels of data access and security: * Free (public) access (e.g., for data associated with published studies) * Data access restricted to collaborators in different laboratories * Owner-only access for work in progress Data can be downloaded from SumsDB as individual files or as bundles archived for offline visualization and analysis in Caret WebCaret provides online Caret-style visualization while circumventing software and data downloads. It is a server-side application running on a linux cluster at Washington University. WebCaret "scenes" facilitate rapid visualization of complex combinations of data Bi-directional links between online publications and WebCaret/SumsDB provide: * Links from figures in online journal article to corresponding scenes in WebCaret * Links from metadata in WebCaret directly to relevant online publications and figures | segmentation, volume, neuroimaging, brain, fmri, stereotaxic foci, stereotaxic coordinate, brain-mapping, foci, structural mri, mri, cerebral cortex, cerebellar cortex, afni brik, analyze, atlas, nifti, registration, rendering, spatial transformation, surface analysis, surface rendering, visualization, volume rendering, brain mapping, neuroanatomy |
is used by: NIF Data Federation is listed by: Biositemaps is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: re3data.org is related to: Computerized Anatomical Reconstruction and Editing Toolkit is related to: Integrated Manually Extracted Annotation has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA |
Mental disease, Neurological disorder, Normal | Human Brain Project ; NSF ; NCI ; NLM ; NASA ; National Partnership for Advanced Computational Infrastructure ; NIMH R01 MH60974-06 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00016, r3d100010169 | http://brainvis.wustl.edu/wiki/index.php/Sums:About http://www.nitrc.org/projects/sumsdb, https://doi.org/10.17616/R3JC76 | SCR_002759 | SumsDB WebCaret, SumsDB Database, Web Caret, WebCaret Online Visualization, Surface Management System Database and WebCaret Online Visualization, SumsDB and WebCaret, Sums database, SumsDB (Surface Management System Database) and WebCaret Online Visualization, Sums DB, SumsDB (Surface Management System Database) WebCaret Online Visualization, Surface Management System Database | 2026-09-05 06:24:53 | 14 | ||||
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TRANSPATH Resource Report Resource Website 1+ mentions |
TRANSPATH (RRID:SCR_005640) | TRANSPATH | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Database on eukaryotic transcription factors, their experimentally-proven binding sites, consensus binding sequences (positional weight matrices) and regulated genes. Its broad compilation of binding sites allows the derivation of positional weight matrices. It can either be used as an encyclopedia, for both specific and general information on signal transduction, or can serve as a network analyzer. Cross-references to important sequence and signature databases such as EMBL/GenBank UniProt/Swiss-Prot InterPro or Ensembl EntrezGene RefSeq are provided. The database is equipped with the tools for data visualization and analysis. It has three modules: the first one is the data, which have been manually extracted, mostly from the primary literature; the second is PathwayBuilder, which provides several different types of network visualization and hence facilitates understanding; the third is ArrayAnalyzer, which is particularly suited to gene expression array interpretation, and is able to identify key molecules within signalling networks (potential drug targets). These key molecules could be responsible for the coordinated regulation of downstream events. Manual data extraction focuses on direct reactions between signalling molecules and the experimental evidence for them, including species of genes/proteins used in individual experiments, experimental systems, materials and methods. This combination of materials and methods is used in TRANSPATH to assign a quality value to each experimentally proven reaction, which reflects the probability that this reaction would happen under physiological conditions. Another important feature in TRANSPATH is the inclusion of transcription factor-gene relations, which are transferred from TRANSFAC, a database focused on transcription regulation and transcription factors. Since interactions between molecules are mainly direct, this allows a complete and stepwise pathway reconstruction from ligands to regulated genes. | signal transduction, network analyzer, transcriptional regulator, transcription factor, metabolic pathway, signaling pathway, protein-protein interaction, gene-regulatory pathway, signal transduction pathway, complex, signaling molecule, reaction, molecule, gene, pathway, gene expression |
is related to: TRANSFAC is related to: GeneTrail has parent organization: BIOBASE Corporation |
BMBF 031U210B; BMBF 0313092; European Union FP6 contract LSHG-CT-2004-503568; European Union MRTN-CT-2004-512285 |
PMID:18629064 PMID:16381929 PMID:12519957 PMID:11724734 |
Free for academic use, Free for non-profit use, Account required | nif-0000-03580 | http://transpath.gbf.de, http://www.gene-regulation.com/pub/databases.html, http://www.biobase.de/pages/products/databases.html | SCR_005640 | 2026-09-05 06:25:39 | 3 | |||||
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GeneMANIA Resource Report Resource Website 1000+ mentions |
GeneMANIA (RRID:SCR_005709) | GeneMANIA | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource, software resource | Data analysis service to predict the function of your favorite genes and gene sets. Indexing 1,421 association networks containing 266,984,699 interactions mapped to 155,238 genes from 7 organisms. GeneMANIA interaction networks are available for download in plain text format. GeneMANIA finds other genes that are related to a set of input genes, using a very large set of functional association data. Association data include protein and genetic interactions, pathways, co-expression, co-localization and protein domain similarity. You can use GeneMANIA to find new members of a pathway or complex, find additional genes you may have missed in your screen or find new genes with a specific function, such as protein kinases. Your question is defined by the set of genes you input. If members of your gene list make up a protein complex, GeneMANIA will return more potential members of the protein complex. If you enter a gene list, GeneMANIA will return connections between your genes, within the selected datasets. GeneMANIA suggests annotations for genes based on Gene Ontology term enrichment of highly interacting genes with the gene of interest. GeneMANIA is also a gene recommendation system. GeneMANIA is also accessible via a Cytoscape plugin, designed for power users. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | gene, association data, protein interaction, genetic interaction, pathway, co-expression, co-localization, protein, software library, statistical analysis, term enrichment, analysis, browser, gene ontology, gene predicting, gene prioritization, database or data warehouse, other analysis, interaction browser, protein-protein interaction, interaction, FASEB list |
is listed by: Gene Ontology Tools is related to: Cytoscape is related to: Gene Ontology is related to: PSICQUIC Registry has parent organization: University of Toronto; Ontario; Canada |
Genome Canada ; Ontario Ministry of Research and Innovation 2007-OGI-TD-05 |
PMID:20576703 PMID:18613948 PMID:20926419 |
Open unspecified license, Free for academic use | nlx_149159, r3d100013978 | https://doi.org/10.17616/R31NJNA2 | SCR_005709 | 2026-09-05 06:25:40 | 4535 | |||||
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GoFish Resource Report Resource Website 1+ mentions |
GoFish (RRID:SCR_005682) | GoFish | analysis service resource, data analysis service, production service resource, service resource, software resource, source code | Software program, available as a Java applet online or to download, allows the user to select a subset of Gene Ontology (GO) attributes, and ranks genes according to the probability of having all those attributes., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, ontology or annotation browser, java, windows, mac os x, linux, unix, bio.tools |
is listed by: Gene Ontology Tools is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: University of Toronto; Ontario; Canada has parent organization: Harvard Medical School; Massachusetts; USA |
Aventis Pharmaceuticals ; Howard Hughes Medical Institute ; NHGRI |
PMID:12691998 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:gofish, nlx_149126, OMICS_02272 | http://llama.mshri.on.ca/Software.html, https://bio.tools/gofish | SCR_005682 | 2026-09-05 06:25:40 | 1 | |||||
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BrainStars Resource Report Resource Website 10+ mentions |
BrainStars (RRID:SCR_005810) | B* | data access protocol, data or information resource, database, software resource, web service | BrainStars (or B*) is a quantitative expression database of the adult mouse brain. The database has genome-wide expression profile at 51 adult mouse CNS regions. For 51 CNS regions, slices (0.5-mm thick) of mouse brain were cut on a Mouse Brain Matrix, frozen, and the specific regions were punched out bilaterally with a microdissecting needle (gauge 0.5 mm) under a stereomicroscope. For each region, we took samples every 4 hours, starting at ZT0 (Zeitgaber time 0; the time of lights on), for 24 hours (6 time-point samples for each region), and we pooled the samples from the different time points. We independently sampled each region twice (n=2). These samples were purified their RNA, and measured with Affymetrix GeneChip Mouse Genome 430 2.0 arrays. Expression values were then summarized with the RMA method. After several analysis with the expression data, the data and analysis results were stored in the BrainStars database. The database has a REST-like Web API interface for accessing from your Web applications. This document shows how to access the database via our Web API. | mouse, brain, adult, expression profile, affymetrix genechip mouse genome 430 2.0 array, rna, central nervous system, gene expression, gene |
is related to: Allen Mouse Brain Reference Atlas is related to: Allen Institute for Brain Science has parent organization: RIKEN has parent organization: Kindai University School of Medicine; Osaka; Japan |
Japanese Ministry of Education Culture Sports Science and Technology MEXT | PMID:21858037 | BrainStars data, Images and texts (excluding ABA data and images) are licensed under a Creative Commons Attribution 2.1 Japan License. | nlx_149301 | SCR_005810 | BrainStars Database, BrainStars (B*) | 2026-09-05 06:25:42 | 15 | |||||
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GREAT: Genomic Regions Enrichment of Annotations Tool Resource Report Resource Website 50+ mentions |
GREAT: Genomic Regions Enrichment of Annotations Tool (RRID:SCR_005807) | GREAT | analysis service resource, data analysis service, production service resource, service resource, software resource, source code | Data analysis service that predicts functions of cis-regulatory regions identified by localized measurements of DNA binding events across an entire genome. Whereas previous methods took into account only binding proximal to genes, GREAT is able to properly incorporate distal binding sites and control for false positives using a binomial test over the input genomic regions. GREAT incorporates annotations from 20 ontologies and is available as a web application. The utility of GREAT extends to data generated for transcription-associated factors, open chromatin, localized epigenomic markers and similar functional data sets, and comparative genomics sets. Platform: Online tool | term enrichment, cis-regulatory region, function, gene, genomic, annotation, ontology, chromatin immunoprecipitation, sequencing, chip-seq, comparative genomics, transcription factor binding |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: PRISM (Stanford database) is related to: Gene Ontology has parent organization: Stanford University School of Medicine; California; USA |
Bio-X ; Howard Hughes Medical Institute ; Stanford University; California; USA ; Packard ; Searle Scholar ; Microsoft Research ; Alfred P. Sloan Foundation ; Edward Mallinckrodt Jr. Foundation ; NIH ; Human Frontier Science Program fellowship LT000896/2009-l; NICHD 1R01HD059862; NHGRI R01HG005058; NSF CCF-0939370; DFG Hi 1423/2-1 |
PMID:20436461 PMID:23814184 |
Free for academic use, Acknowledgement requested | nlx_149295, OMICS_00635 | SCR_005807 | Genomic Regions Enrichment of Annotations Tool (GREAT), Genomic Regions Enrichment of Annotations Tool | 2026-09-05 06:25:42 | 89 | |||||
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OCDM - Ontology of Craniofacial Development and Malformation Resource Report Resource Website 1+ mentions |
OCDM - Ontology of Craniofacial Development and Malformation (RRID:SCR_005999) | OCDM | controlled vocabulary, data or information resource, ontology | To satisfy the need for standardized terminologies several ontologies, we are developing the Ontology of Craniofacial Development and Malformation. When complete, this ontology will describe several realms of anatomy and development relevant to FaceBase, including: * Human craniofacial anatomy, including developmental progressions * Craniofacial malformations * Mouse craniofacial anatomy * Mappings between mouse and human anatomy These ontologies are currently undergoing active development. As a result, these files should be considered very preliminary. They may not work correctly, and contents will almost certainly undergo significant change. Five (sub) ontologies in this zip archive correspond to the categories described above. * OCDM - Ontology of Craniofacial Development and Malformation: currently imports the CHO, CMO, and the CHMMO. * CHO - Craniofacial Human Ontoloogy: normal adult human craniofacial anatomy derived from the FMA. * CMO - Craniofacial Mouse Ontology: normal adult mouse craniofacial anatomy * CHMMO - Craniofacial Human-Mouse Mapping Ontology: mappings of classes in the * CHO to related (homologous) structures in the CMO. CFMO - Craniofacial Malformation Ontology: abnormal human anatomy, includes the CHO All ontologies are in Protege Frames format (requires Protege 3.x). Ontologies refer to other ontologies via the Protege include mechanism. The CHMMO includes the CHO and the CMO. The OCDM (which is the umbrella ontology) includes all of the rest. Future releases will include translations to the OWL language. | craniofacial development, malformation, craniofacial malformation, anatomy | has parent organization: FaceBase | nlx_151377 | SCR_005999 | Ontology of Craniofacial Development Malformation (OCDM), Ontology of Craniofacial Development and Malformation (OCDM), OCDM - Ontology of Craniofacial Development Malformation | 2026-09-05 06:25:45 | 1 | ||||||||
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Allen Brain Atlas API Resource Report Resource Website 10+ mentions |
Allen Brain Atlas API (RRID:SCR_005984) | Allen Brain Atlas API | data or information resource, portal, software application, software resource, source code, topical portal | API and demo application for accessing the Allen Brain Atlas Mouse Brain data. Data available via the API includes download high resolution images, expression data from a 3D volume, 3D coordinates of the Allen Reference Atlas, and searching genes with similar gene expression profiles using NeuroBlast. Data made available includes: * High resolution images for gene expression, connectivity, and histology experiments, as well as annotated atlas images * 3-D expression summaries registered to a reference space for the Mouse Brain and Developing Mouse Brain * Primary microarray results for the Human Brain and Non-Human Primate * RNA sequencing results for the Developing Human Brain * MRI and DTI files for Human Brain The API consists of the following resources: * RESTful model access * Image download service * 3-D expression summary download service * Differential expression search services * NeuroBlast correlative searches * Image-to-image synchronization service * Structure graph download service | atlas application, expression data, 3d volume, 3d coordinate, gene, reference atlas, connectivity, histology, microarray, brain, rna sequencing, mri, dti, api, computational neuroscience, mouse brain, neuroanatomy, neuroimaging, neuroinformatics, ish, high resolution image, nissl, annotation, atlas, image, web service, neuroblast, gene expression, gene, computational neuroscience, mouse brain, neuroanatomy, neuroimaging, neuroinformatics |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Allen Mouse Brain Reference Atlas is related to: Allen Developing Mouse Brain Atlas is related to: International Neuroinformatics Coordinating Facility is related to: Brain Explorer Atlas and Teaching Tool is related to: CellTax vignette is related to: Allen Mouse Brain Common Coordinate Framework has parent organization: Allen Institute for Brain Science |
Other/Commercial license License | nlx_151358 | http://www.nitrc.org/projects/incf_allen-brai | SCR_005984 | 2026-09-05 06:25:45 | 13 | |||||||
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Mammalian Adult Neurogenesis Gene Ontology Resource Report Resource Website 50+ mentions |
Mammalian Adult Neurogenesis Gene Ontology (RRID:SCR_006176) | MANGO | controlled vocabulary, data or information resource, database, ontology | Database of genes concerning adult neurogenesis mapped to cell types and processes that have been curated from the literature. In its present state, the database is restricted to neurogenesis in the hippocampus. | adult neurogenesis, adult, neurogenesis, hippocampus, gene, annotation, cell type, process, FASEB list | has parent organization: Dresden University of Technology; Saxony; Germany | nlx_151684 | SCR_006176 | 2026-09-05 06:25:48 | 64 | |||||||||
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NHMRC Australian PhenomeBank Resource Report Resource Website 1+ mentions |
NHMRC Australian PhenomeBank (RRID:SCR_006149) | APB | biomaterial supply resource, cell repository, material resource, organism supplier | The NHMRC Australian PhenomeBank (APB) is a non-profit repository of mouse strains used in Medical Research. The database allows you to search for murine strains, housed or archived in Australia, carrying mutations in particular genes, strains with transgenic alterations and for mice with particular phenotypes. 1876 publicly available strains, 922 genes, 439 transgenes The APB has two roles: Provide and maintain a central database of genetically modified mice held in Australia either live or as cryopreserved material; Establish and maintain a mouse strain archive. Strains are archived as cryopreserved sperm or embryos. | RIN, Resource Information Network, murine, mutation, gene, strain, transgenic, alteration, phenotype, live mouse, sperm, embryo, transgene, database, allele, chromosome, RRID Community Authority |
is listed by: One Mind Biospecimen Bank Listing is listed by: Resource Information Network has parent organization: Australian Phenomics Network works with: International Mouse Strain Resource |
Public | nlx_151640 | http://pb.apf.edu.au/phenbank/foreignPageImport.html?page=http://pbstatic.apf.edu.au:80/phenbank/home.htm | SCR_006149 | Australian Phenome Bank, Phenome Bank, Australian PhenomeBank, NHMRC Australian Phenome Bank, PhenomeBank | 2026-09-05 06:25:48 | 3 | ||||||
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European Mouse Mutant Archive Resource Report Resource Website 50+ mentions |
European Mouse Mutant Archive (RRID:SCR_006136) | EMMA | biomaterial supply resource, material resource, organism supplier | Non-profit repository for the collection, archiving (via cryopreservation) and distribution of relevant mutant strains essential for basic biomedical research. Users may browse by strain, gene, phenotype, or human disease. Its primary objective is to establish and manage a unified repository for maintaining medically relevant mouse mutants and making them available to the scientific community. Therefore, EMMA archives mutant strains and distributes them to requesting researchers. EMMA also hosts courses in cryopreservation, to promote the use and dissemination of frozen embryos and spermatozoa. Dissemination of knowledge is further fostered by a dedicated resource database. Anybody who wants their mutant mouse strains cryopreserved may deposit strains with EMMA. However depositors must be aware that these strains become freely available to other researchers after being deposited.With more than 8400 mutant mouse strains and asmall but increasing number of rat mutant strains available, EMMA is the primary mouse repository in Europe and the third largest non-profit repository worldwide. | RIN, Resource Information Network, mutant mouse repository, mouse, mutant strain, mutant mouse strain, , RRID Community Authority |
is used by: EUCOMMTOOLS is listed by: One Mind Biospecimen Bank Listing is listed by: Resource Information Network is related to: European Conditional Mouse Mutagenesis Program is related to: International Knockout Mouse Consortium is related to: Federation of International Mouse Resources is related to: MGI strains has parent organization: Helmholtz Center Munich Institute of Experimental Genetics works with: International Mouse Strain Resource |
partner institutions ; national research programmes ; European Union |
PMID:19783817 PMID:17709347 |
Public, Free to researchers | nlx_151625 | https://www.infrafrontier.eu | emmanet.org | SCR_006136 | European Mouse Mutant Archive - EMMA, European Mouse Mutant Archive (EMMA) | 2026-09-05 06:25:47 | 64 | |||
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Federation of International Mouse Resources Resource Report Resource Website 1+ mentions |
Federation of International Mouse Resources (RRID:SCR_006137) | FIMRe | community building portal, data or information resource, portal, topical portal | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 7, 2022. Federation of International Mouse Resources (FIMRe) is a collaborating group of Mouse Repository and Resource Centers worldwide whose collective goal is to archive and provide strains of mice as cryopreserved embryos and gametes, ES cell lines, and live breeding stock to the research community. Goals of the Federation of International Mouse Resources: * Coordinate repositories and resource centers to: ** archive valuable genetically defined mice and ES cell lines being created worldwide ** meet research demand for these genetically defined mice and ES cell lines * Establish consistent, highest quality animal health standards in all resource centers * Provide genetic verification and quality control for genetic background and mutations * Provide resource training to enhance user ability to utilize cryopreserved resources | embryo, gamete, embryonic stem cell, embryonic stem cell line, live breeding stock, live mouse, resource center, international network, mouse model, human disease, gene, genome, biomaterial supply resource, cell repository, organism supplier, biospecimen repository, mutation, cryopreserved |
is related to: Jackson Laboratory is related to: Mutant Mouse Resource and Research Center is related to: European Mouse Mutant Archive is related to: RIKEN BioResource Center has parent organization: Mouse Genome Informatics (MGI) |
PMID:16688526 | THIS RESOURCE IS NO LONGER IN SERVICE. | nlx_151627 | SCR_006137 | Federation of International Mouse Resources (FIMRe) | 2026-09-05 06:25:47 | 4 | ||||||
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StemBase Resource Report Resource Website 1+ mentions |
StemBase (RRID:SCR_006252) | StemBase | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | A publicly accessible database containing data on Affymetrix DNA microarray experiments, and Serial Analysis of Gene Expression, mostly on human and mouse stem cell samples and their derivatives to facilitate the discovery of gene functions relevant to stem cell control and differentiation. It has grown in both size and scope into a system with analysis tools that examine either the whole database at once, or slices of data, based on tissue type, cell type or gene of interest. There is currently more than 210 stem cell samples in 60 different experiments, with more being added regularly. The samples were originated by researchers of the Stem Cell Network and processed at the Core Facility of Stemcore Laboratories under the management of Ms. Pearl Campbell in the frame of the Stem Cell Genomics Project. Periodically, new expression data is submitted to the Gene Expression Omnibus (GEO) repository at the National Center for Biotechnological Information, in order to allow researchers to compare the data deposited in StemBase to a large amount of gene expression data sets. StemBase is different from GEO in both focus and scope. StemBase is concerned exclusively with stem cell related data. we are focused in Stem Cell research. We have made a significant effort to ensure the quality and consistency of the data included. This allows us to offer more specialized analysis tools related to Stem Cell data. GEO is intended as a large scale public archive. Deposition in a public repository such as GEO is required by most important scientific journals and it is advantageous for a further diffusion of the data since GEO is more broadly used than StemBase. | stem cell, gene expression, dna microarray, correlation tool, serial analysis of gene expression, correlation |
is used by: BloodExpress has parent organization: University of Ottawa; Ontario; Canada |
Genome Canada ; Canadian Stem Cell Network ; Canadian Institutes of Health Research ; Canada Research Chairs |
PMID:19284540 PMID:18453254 PMID:15763554 |
Publicly accessible. Please cite. | nlx_151919 | SCR_006252 | Stem Cell Genomics database | 2026-09-05 06:25:49 | 4 | |||||
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Impress Resource Report Resource Website 50+ mentions |
Impress (RRID:SCR_006160) | IMPReSS | data access protocol, data or information resource, experimental protocol, international standard specification, narrative resource, software resource, standard specification, web service | Contains standardized phenotyping protocols essential for the characterization of mouse phenotypes. IMPReSS holds definitions of the phenotyping Pipelines and mandatory and optional Procedures and Parameters carried out and data collected by international mouse clinics following the protocols defined. This allows data to be comparable and shareable and ontological annotations permit interspecies comparison which may help in the identification of phenotypic mouse-models of human diseases. The IMPC (International Mouse Phenotyping Consortium) core pipeline describes the phenotype pipeline that has been agreed by the research institutions. IMPReSS has a SOAP web service machine interface. The WSDL can be accessed here: http://www.mousephenotype.org/impress/soap/server?wsdl | phenotype, phenotyping, adult, embryonic, ontology, enu-induced gene knockout, gene, knockout mouse, ethylnitrosourea |
is related to: European Mouse Phenotyping Resource of Standardised Screens has parent organization: International Mouse Phenotyping Consortium (IMPC) |
nlx_151661 | SCR_006160 | International Mouse Phenotyping Resource of Standardised Screens, IMPReSS - International Mouse Phenotyping Resource of Standardised Screens | 2026-09-05 06:25:48 | 66 | ||||||||
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Mutant Mouse Resource and Research Center Resource Report Resource Website 1000+ mentions |
Mutant Mouse Resource and Research Center (RRID:SCR_002953) | MMRRC | biomaterial supply resource, material resource, organism supplier | National public repository system for mutant mice. Archives and distributes scientifically valuable spontaneous and induced mutant mouse strains and ES cell lines for use by biomedical research community. Includes breeding/distribution facilities and information coordinating center. Mice strains are cryopreserved, unless live colony must be established. Live mice are supplied from production colony, from colony recovered from cryopreservation, or via micro-injection of cell line into host blastocysts. MMRRC member facilities also develop technologies to improve handling of mutant mice, including advances in assisted reproductive techniques, cryobiology, genetic analysis, phenotyping and infectious disease diagnostics. | RIN, Resource Information Network, stem cell, mouse strain, embryonic stem cell, embryonic stem cell line, cryopreserved, mutant mouse strain, mutant, transgenic, database, FASEB list, RRID Community Authority |
is used by: Integrated Animals is listed by: One Mind Biospecimen Bank Listing is listed by: Biositemaps is listed by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: NIDDK Research Resources is listed by: NIDDK Information Network (dkNET) is listed by: Resource Information Network is affiliated with: MUGA is affiliated with: MegaMUGA is related to: Federation of International Mouse Resources is related to: Mouse Mutagenesis Center for Developmental Defects is related to: MGI strains has parent organization: Jackson Laboratory has parent organization: University of California at Davis; California; USA has parent organization: University of Missouri; Missouri; USA has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA has parent organization: National Institutes of Health is parent organization of: Deltagen and Lexicon Knockout Mice and Phenotypic Data Resource provides: Knockout Mouse Project Repository has organization facet: University of California at Davis Mutant Mouse Resource and Research Center has organization facet: Mutant Mouse Resource and Research Center - University of North Carolina has organization facet: Mutant Mouse Resource and Research Center - University of Missouri has organization facet: Mutant Mouse Resource and Research Center - Jackson Laboratory |
NCRR RR026296; NIH Blueprint for Neuroscience Research ; NIH Office of the Director U42 OD010918; NIH Office of the Director U42 OD010921; NIH Office of the Director U42 OD010924; NIH Office of the Director U42 OD012210 |
Restricted | nif-0000-00045 | SCR_002953 | Mutant Mouse Regional Resource Center | 2026-09-05 06:24:56 | 1079 | ||||||
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I2D Resource Report Resource Website 10+ mentions |
I2D (RRID:SCR_002957) | I2D | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Database of known and predicted mammalian and eukaryotic protein-protein interactions, it is designed to be both a resource for the laboratory scientist to explore known and predicted protein-protein interactions, and to facilitate bioinformatics initiatives exploring protein interaction networks. It has been built by mapping high-throughput (HTP) data between species. Thus, until experimentally verified, these interactions should be considered predictions. It remains one of the most comprehensive sources of known and predicted eukaryotic PPI. It contains 490,600 Source Interactions, 370,002 Predicted Interactions, for a total of 846,116 interactions, and continues to expand as new protein-protein interaction data becomes available. | interaction, prediction, protein-protein interaction, high-throughput, model organism, mammal, eukaryote, visualization, interolog, protein |
is related to: Interaction Reference Index is related to: IMEx - The International Molecular Exchange Consortium is related to: PSICQUIC Registry is related to: IntAct has parent organization: University of Toronto; Ontario; Canada |
National Science and Engineering Research Council RGPIN 203833-02; NIGMS P50-GM62413 |
PMID:17535438 PMID:15657099 |
Free, Available for download, Freely available | nif-0000-03005, r3d100010675 | https://doi.org/10.17616/R3BG8R | SCR_002957 | Interologous Interaction Database, OPHID, I2D - Interologous Interaction Database | 2026-09-05 06:24:56 | 23 | ||||
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Special Mouse Strains Resource Resource Report Resource Website |
Special Mouse Strains Resource (RRID:SCR_002885) | SMSR | biomaterial supply resource, material resource, organism supplier | Resource of special strains of mice that are valuable tools for genetic analysis of complex diseases. They include panels of recombinant inbred (RI) and chromosome substitution (CS) strains. | strain panel, frozen, cryopreserved, recombinant inbred mouse, chromosome substitution mouse, consomic strain, gene, disease, strain |
is listed by: One Mind Biospecimen Bank Listing is related to: One Mind Biospecimen Bank Listing is related to: Mouse Phenome Database (MPD) has parent organization: Jackson Laboratory |
Recombinant inbred mouse, Chromosome substitution mouse, Consomic strain | NCRR P40 RR016049; NIH Office of the Director P40 OD011102 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-25593 | SCR_002885 | Special Mouse Strains Resource (SMSR) | 2026-09-05 06:24:55 | 0 | |||||
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GenePaint Resource Report Resource Website 100+ mentions |
GenePaint (RRID:SCR_003015) | GenePaint.org | atlas, data or information resource, database, expression atlas, reference atlas | Digital atlas of gene expression patterns in developing and adult mouse. Several reference atlases are also available through this site. Expression patterns are determined by non-radioactive in situ hybridization on serial tissue sections. Sections are available from several developmental ages: E10.5, E14.5 (whole embryos), E15.5, P7 and P56 (brains only). To retrieve expression patterns, search by gene name, site of expression, GenBank accession number or sequence homology. For viewing expression patterns, GenePaint.org features virtual microscope tool that enables zooming into images down to cellular resolution. | gene expression, adult mouse, annotated, c57bl6, mouse, mouse embryo, mrna, non radioactive in situ hybridization, light microscopy, molecular neuroanatomy resource, in situ hybridization, embryonic, postnatal, adult, brain, head, annotation, rna probe, sequence, anatomical structure, FASEB list |
has parent organization: Max Planck Institute for Biophysical Chemistry; Gottingen; Germany is parent organization of: GenePaint E15 Atlas is parent organization of: GenePaint P7 Atlas is parent organization of: GenePaint P56 Mouse Atlas is parent organization of: GenePaint Interactive Anatomy Atlas |
BMBF ; Burroughs Wellcome Fund ; European Union ; Max Planck Society ; Merck Genome Research Institute ; NINDS ; Romansky Endowment |
PMID:14681479 PMID:22936000 |
nif-0000-00009, SCR_017526 | SCR_003015 | Atlas of Gene Expression Patterns in Mouse Embryo | 2026-09-05 06:24:56 | 164 | ||||||
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JAX Neuroscience Mutagenesis Facility Protocols Resource Report Resource Website |
JAX Neuroscience Mutagenesis Facility Protocols (RRID:SCR_003021) | NMF Protocols | data or information resource, experimental protocol, narrative resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. The Neuroscience Mutagenesis Facility of the Jackson Laboratory (NMF) was established to produce new neurological mouse models that could serve as experimental models for the exploration of basic neurobiological mechanisms and diseases. The protocols are available. The impetus for the program resulted from the recognition that * the value of genomic data would remain limited unless more information about the functionality of its individual components became available, and * the task of linking genes to specific behavior would best be accomplished by employing a combination of different approaches. In an effort to complement already existing programs, the Neuroscience Mutagenesis Facility decided to use: a random, genome-wide approach to mutagenesis, i.e. N-ethyl-N-nitrosourea (ENU) as the mutagen; a three-generation back-cross breeding scheme to focus on the detection of recessive mutations; behavioral screens selective for the detection of phenotypes deemed useful for the program goals. Protocols: * Genetics ** Production of Mice for a Genome-Wide ENU Mutagenesis Screen ** Production of Mice using Chemical Mutagenesis of Mouse ES Cells * Protocols ** Step by step procedures-- Mouse mutagenesis with ENU ** Step by step procedures-- ES Cell mutagenesis with EMS * Phenotyping: Overview * Protocols:(currently only screens marked * are in use) ** Acoustic startle response (ASR) ** Auditory brainstem response (ABR) ** CLAMSTM(former CCMS) ** Creatine kinase ** Developmental Screen * ** Eye and Vision * ** Gait Analysis ** Gustation ** Observation * ** Seizure threshold * ** Additional Background Information | mutant mouse strain, genetically-modified mouse, motor system function, impairment of function, eye disease, eye disorder, ophthalmological disorder, ophthalmic disorder, ocular disease, disease of eye, epilepsy, epileptic seizure, seizure disorder, gustatory system function, taste system function, bioinformatics, acoustic startle response, auditory brainstem response, creatine kinase, development, eye, vision, gait, gustation, observation, seizure, mutagenesis, n-ethyl-n-nitrosourea, es cell mutagenesis, ems, genetics, phenotyping | has parent organization: JAX Neuroscience Mutagenesis Facility | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00527 | SCR_003021 | JAX Protocols, Protocols of the NMF, Protocols of the Neuroscience Mutagenesis Facility, JAX NMF Protocols | 2026-09-05 06:24:56 | 0 |
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