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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Drug Related Gene Database Resource Report Resource Website 1+ mentions |
Drug Related Gene Database (RRID:SCR_003330) | DRG | data or information resource, database | Gene expression data from published journal articles that test hypotheses relevant to neuroscience of addiction and addictive behavior. Data types include effects of particular drug, strain, or knock out on particular gene, in particular anatomical region. Focuses on gene expression data and exposes data from investigations using DNA microarrays, polymerase chain reaction, immunohistochemistry and in-situ hybridizations. Data are available for query through NIF interface.Data submissions are welcome. | drug of abuse, gene expression, brain region, brain, american recovery and reinvestment act, brain, dna microarray, microarray, addiction |
uses: PubMed is listed by: NIF Data Federation is related to: Integrated Manually Extracted Annotation has parent organization: Neuroscience Information Framework |
NIDA | Free, Freely available | nif-0000-37443 | https://confluence.crbs.ucsd.edu/login.action?os_destination=%2Fpages%2Fviewpage.action%3FspaceKey%3DNIF%26title%3DDRG&permissionViolation=true | SCR_003330 | DRG Database, Drug Dependent Gene Database | 2026-07-28 09:40:40 | 2 | |||||
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Public Expression Profiling Resource Resource Report Resource Website 10+ mentions |
Public Expression Profiling Resource (RRID:SCR_007274) | PEPR | data or information resource, database | An experiment in web-database access to large multi-dimensional data sets using a standardized experimental platform to determine if the larger scientific community can be given simple, intuitive, and user-friendly web-based access to large microarray data sets. All data in PEPR is also available via NCBI GEO. The structure and goals of PEPR differ from other mRNA expression profiling databases in a number of important ways. * The experimental platform in PEPR is standardized, and is an Affymetrix - only database. All microarrays available in the PEPR web database should ascribe to quality control and standard operating procedures. A recent publication has described the QC/SOP criteria utilized in PEPR profiles ( The Tumor Analysis Best Practices Working Group 2004 ). * PEPR permits gene-based queries of large Affymetrix array data sets without any specialized software. For example, a number of large time series projects are available within PEPR, containing 40-60 microarrays, yet these can be simply queried via a dynamic web interface with no prior knowledge of microarray data analysis. * Projects in PEPR originate from scientists world-wide, but all data has been generated by the Research Center for Genetic Medicine, Children''''s National Medical Center, Washington DC. Future developments of PEPR will allow remote entry of Affymetrix data ascribing to the same QC/SOP protocols. They have previously described an initial implementation of PEPR, and a dynamic web-queried time series graphical interface ( Chen et al. 2004 ). A publication showing the utility of PEPR for pharmacodynamic data has recently been published ( Almon et al. 2003 ). | microarray, expression profiling, affymetrix, metadata standard, gene, time series, data sharing, visualization, data mining, platform, blood, cell, cancer, bone, brain, eye, gut, heart, kidney, liver, lung, muscle, spinal cord, spleen, analysis |
is listed by: OMICtools is related to: Gene Expression Omnibus |
NINDS ; United States Department of Defense ; NHGRI ; NHLBI |
PMID:14681485 PMID:14596642 |
Public, Account required, (to download, For the analysis and visualization tools), The community can contribute to this resource | nif-0000-00014, OMICS_00776 | SCR_007274 | 2026-07-28 09:41:46 | 16 | ||||||
|
ChimerDB Resource Report Resource Website 10+ mentions |
ChimerDB (RRID:SCR_007596) | data or information resource, database | Knowledgebase of fusion transcripts collected from various public resources such as the Sanger CGP, OMIM, PubMed, and Mitelman's database. It is an alignment viewer to facilitate examining reliability of fusion transcripts and inferring functional significance., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | knowledge base, fusion transcript, transcript alignment, alignment viewer | has parent organization: Ewha Womans University; Seoul; South Korea | Tumor, Cancer | Korean Ministry of Education Science and Technology ; Gwangju Institute of Science and Technology ; Korean Ministry of Science and Technology R01-2008-000-20818-0; Korean Ministry of Science and Technology 2007-03983; National Core Research Center R15-2006-020; Korean Rural Development Administration 20070401034010 |
PMID:19906715 PMID:16381848 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02659 | http://genome.ewha.ac.kr/ChimerDB/ | SCR_007596 | 2026-07-28 09:41:51 | 29 | |||||
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Mammalian Degradome Database Resource Report Resource Website 10+ mentions |
Mammalian Degradome Database (RRID:SCR_007624) | Degradome Database | data or information resource, database | A database of human, chimpanzee, mouse, and rat proteases and protease inhibitors, as well as as the growing number of hereditary diseases caused by mutations in protease genes. Analysis of the human and mouse genomes has allowed us to annotate 581 human, 580 chimpanzee, 667 mouse, and 655 rat protease genes. Proteases are classified in five different classes according to their mechanism of catalysis. Proteases are a diverse and important group of enzymes representing >2% of the human, chimpanzee, mouse and rat genomes. This group of enzymes is implicated in numerous physiological processes. The importance of proteases is illustrated by the existence of 99 different hereditary diseases due to mutations in protease genes. Furthermore, proteases have been implicated in multiple human pathologies, including vascular diseases, rheumatoid arthritis, neurodegenerative processes, and cancer. During the last ten years, our laboratory has identified and characterized more than 60 human protease genes. Due to the importance of proteolytic enzymes in human physiology and pathology, we have recently introduced the concept of Degradome, as the complete repertoire of proteases expressed by a tissue or organism. Thanks to the recent completion of the human, chimpanzee, mouse, and rat genome sequencing projects, we were able to analyze and compare for the first time the complete protease repertoire in those mammalian organisms, as well as the complement of protease inhibitor genes. This webpage also contains the Supplementary Material of Human and mouse proteases: a comparative genomic approach Nat Rev Genet (2003) 4: 544-558, Genome sequence of the brown Norway rat yields insights into mammalian evolution Nature (2004) 428: 493-521, A genomic analysis of rat proteases and protease inhibitors Genome Res. (2004) 14: 609-622, and Comparative genomic analysis of human and chimpanzee proteases Genomics (2005) 86: 638-647. | degradome, mammalian, protease inhibitor, protease, gene, protease gene, genetic disease, proteolysis, protease structure, ancillary domain, genomic, genome |
is related to: Ancillary Domains Associated With Human and Mouse Proteases has parent organization: University of Oviedo; Oviedo; Spain |
Disease of proteolysis | European Union ; CancerDegradome-FP6 and FP7 ; Spanish Ministry of Science and Innovation ; Fundacion M Botin ; Fundacion Lilly ; Obra Social Cajastur |
PMID:18776217 | nif-0000-02746 | SCR_007624 | Mammalian Degradome Database | 2026-07-28 09:41:52 | 10 | |||||
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ECgene: Gene Modeling with Alternative Splicing Resource Report Resource Website 10+ mentions |
ECgene: Gene Modeling with Alternative Splicing (RRID:SCR_007634) | ECgene | data or information resource, database | Database of functional annotation for alternatively spliced genes. It uses a gene-modeling algorithm that combines the genome-based expressed sequence tag (EST) clustering and graph-theoretic transcript assembly procedures. It contains genome, mRNA, and EST sequence data, as well as a genome browser application. Organisms included in the database are human, dog, chicken, fruit fly, mouse, rhesus, rat, worm, and zebrafish. Annotation is provided for the whole transcriptome, not just the alternatively spliced genes. Several viewers and applications are provided that are useful for the analysis of the transcript structure and gene expression. The summary viewer shows the gene summary and the essence of other annotation programs. The genome browser and the transcript viewer are available for comparing the gene structure of splice variants. Changes in the functional domains by alternative splicing can be seen at a glance in the transcript viewer. Two unique ways of analyzing gene expression is also provided. The SAGE tags deduced from the assembled transcripts are used to delineate quantitative expression patterns from SAGE libraries available publicly. The cDNA libraries of EST sequences in each cluster are used to infer qualitative expression patterns. | est cluster, genome, alternative splicing, splice, gene, mrna, est, annotation, gene modeling, structure, function, gene expression, transcript, genome browser, differential expression, snp |
is listed by: OMICtools is related to: Gene Ontology has parent organization: Ewha Womans University; Seoul; South Korea |
PMID:17132829 PMID:15805497 PMID:15608289 |
nif-0000-02780, OMICS_01884 | http://genome.ewha.ac.kr/ECgene/ | SCR_007634 | ECgene - Genome Annotation for Alternative Splicing | 2026-07-28 09:42:08 | 12 | ||||||
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NIA Aged Rodent Tissue Bank Resource Report Resource Website 1+ mentions |
NIA Aged Rodent Tissue Bank (RRID:SCR_010607) | NIA ARTB | tissue bank, biomaterial supply resource, material resource | NIA Aged Rodent Tissue Bank (ARTB) is a repository of tissue collected from mice and rats maintained in the NIA Aged Rodent Colonies. Biospecimens are collected, archived, and distributed under a contractual arrangement with the University of Washington, Seattle. The NIA supports the three R’s of research (Replacement, Reduction, and Refinement) through maximizing the use of existing banked samples from mice and rats and providing tissues for research on aging. Researchers can select frozen tissues, unstained slides from formalin-fixed and paraffin-embedded (FFPE) tissues, or tissue microarrays (TMAs). | tissue, organs, rodent, mouse, rat, aging, aged, flash frozen, frozen, formalin fixed paraffin embedded, FFPE, unstained slides, Tissue Microarray, TMA |
is listed by: One Mind Biospecimen Bank Listing is related to: NIA Aged Rodent Colonies |
National Institute on Aging (NIA) | Tissues from the NIA ARTB are available at no cost to investigators at academic and nonprofit research institutions conducting studies on aging. Investigators at for-profit organizations are not eligible to receive tissues from the NIA ARTB unless they are funded through US federal Small Business Innovation Research (SBIR) or Small Business Technology Transfer (STTR) programs. | nlx_51483 | SCR_010607 | Aged Rodent Tissue Bank, NIA Aged Rodent Tissue Bank at the University of Washington | 2026-07-28 09:42:52 | 1 | ||||||
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Waxholm Space Atlas of the Sprague Dawley Rat Brain Resource Report Resource Website 10+ mentions |
Waxholm Space Atlas of the Sprague Dawley Rat Brain (RRID:SCR_017124) | WHS-SD-atlas | data or information resource, waxholm atlas, atlas | Open access volumetric atlas of anatomical delineations of rat brain based on structural contrast in isotropic magnetic resonance and diffusion tensor images acquired ex vivo from 80 day old male Sprague Dawley rat at Duke Center for In Vivo Microscopy. Spatial reference is provided by Waxholm Space coordinate system. Location of bregma and lambda are identified as anchors towards stereotaxic space. Application areas include localization of signal in non structural images. Atlas, MRI and DTI volumes, and diffusion tensor data are shared in NIfTI format. | volumetric, atlas, anatomical, delineation, rat, brain, structural, contrast, isotropic, MIR, DTI, male, Sprague Dawley, image |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: ITK-SNAP is related to: PMOD Software is related to: Duke University; North Carolina; USA has parent organization: University of Oslo; Oslo; Norway works with: MeshView works with: VisuAlign |
Research Council of Norway ; EC Human Brain Project ; NIBIB P41 EB015897; NCI U24 CA092656 |
PMID:24726336 PMID:25585022 |
Free, Available for download, Freely available | SCR_017124 | WHS SD rat atlas, WHS_SD_rat_atlas, WHS-SD-rat-atlas | 2026-07-28 09:44:27 | 35 | ||||||
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WUSTL School of Medicine Embryonic Stem Cell Core Resource Report Resource Website |
WUSTL School of Medicine Embryonic Stem Cell Core (RRID:SCR_012441) | WUSM Embryonic Stem Cell Core | access service resource, service resource, core facility | The Murine Embryonic Stem Cell Core has been created to help you create mutations in murine embryonic stem cells. The core has several missions including development of state-of-the-art reagents for the production of targeted mutations in embryonic stem cells, the creation of quality-controlled embryonic stem cell lines, and the teaching of methods for embryonic stem cell culture and manipulation. The core utilizes quality-controlled cells developed here at Washington University. |
is listed by: ScienceExchange has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA |
SciEx_13416 | SCR_012441 | WUSTL School of Medicine Murine Embryonic Stem Cell Core, WUSM Murine Embryonic Stem Cell Core | 2026-07-28 09:43:07 | 0 | |||||||||
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Yale Diabetes Research Center Physiology Core Facility Resource Report Resource Website |
Yale Diabetes Research Center Physiology Core Facility (RRID:SCR_015147) | access service resource, service resource, core facility | Fee-for-service core facility for DRC members to facilitate in vivo diabetes-related research dealing with biological outcomes in normal, diabetic, and genetically manipulated rodents and mice. Physiology Core is divided into two Sub-cores: the Animal Surgery and Experimental Procedure Sub-core, which provides assistance with in vivo rodent studies the Analytical Sub-core, which assists with measurement of various analytes in rat and mouse samples. | in vivo diabetes research, rodent studies, diabetes rodents |
is listed by: NIDDK Information Network (dkNET) has parent organization: Yale University; Connecticut; USA has parent organization: Yale Diabetes Research Center is organization facet of: Yale Diabetes Research Center |
Diabetes | NIDDK P30DK045735 | Restricted | SCR_015147 | Yale Diabetes Research Center Physiology Core | 2026-07-28 09:43:59 | 0 | |||||||
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Marion Bessin Liver Research Center Animal Models Stem Cells and Cell Therapy Resource Report Resource Website |
Marion Bessin Liver Research Center Animal Models Stem Cells and Cell Therapy (RRID:SCR_015181) | access service resource, service resource, resource, core facility | Core that provides resources, technologies and scientific expertise to advance translational applications of animal and human liver cells. It also provides bred animals for research, isolation and culture of animal and human liver cells, as well as provision of cell culture additives and materials. | bred animals, animal models, stem cells, liver cells |
is listed by: NIDDK Information Network (dkNET) has parent organization: Albert Einstein College of Medicine; New York; USA has parent organization: Marion Bessin Liver Research Center is organization facet of: Marion Bessin Liver Research Center |
NIDDK P30DK041296 | Available to the research community | SCR_015181 | 2026-07-28 09:43:41 | 0 | |||||||||
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Resource Identification Portal Resource Report Resource Website 10+ mentions |
Resource Identification Portal (RRID:SCR_004098) | RII Portal | data or information resource, portal | Portal providing identifiers for Antibodies, Model Organisms, and Tools (software, databases, services) created in support of the Resource Identification Initiative, which aims to promote research resource identification, discovery, and reuse. The portal offers a central location for obtaining and exploring Research Resource Identifiers (RRIDs) - persistent and unique identifiers for referencing a research resource. A critical goal of the RII is the widespread adoption of RRIDs to cite resources in the biomedical literature and other places that reference their generation or use. RRIDs use established community identifiers where they exist, and are cross-referenced in their system where more than one identifier exists for a single resource. | antibody, organism, service resource, software resource, database, resource, identifier, citation, biomedical, publication, research resource identifier, rrid, ASWG |
uses: Antibody Registry uses: SciCrunch Registry uses: Mouse Genome Informatics (MGI) uses: Zebrafish Information Network (ZFIN) uses: Rat Genome Database (RGD) uses: WormBase uses: FlyBase recommends: SciCrunch Registry recommends: Mouse Genome Informatics (MGI) recommends: Zebrafish Information Network (ZFIN) recommends: Rat Genome Database (RGD) is recommended by: Neuroscience Information Framework is recommended by: SciCrunch Registry is related to: NIF Data Federation has parent organization: SciCrunch |
NIGMS R24 GM144308 | The community can contribute to this resource | nlx_158572 | SCR_004098 | Resource Identification Initiative Portal | 2026-07-28 09:40:54 | 19 | ||||||
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NIDA center for genetic studies of drug abuse in outbred rats Resource Report Resource Website 1+ mentions |
NIDA center for genetic studies of drug abuse in outbred rats (RRID:SCR_021788) | disease-related portal, data or information resource, topical portal, portal | Portal includes information about genetic studies of drug abuse in outbred rats. Data center created in 2014 to perform genome wide association studies on numerous behavioral traits that have well established relevance to drug abuse using outbred rats. | genome wide association studies, outbred rats, genetic studies, drug abuse, behavioral traits | is related to: RatGTEx Portal | addiction | NIDA P50 DA037844 | Free, Freely available | SCR_021788 | NIDA center for GWAS in outbred rats, Genes and Addiction NIDA center for GWAS in outbred rats | 2026-07-28 09:45:22 | 6 |
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Data set from Kravitz, Owen and Kretizer's 2012 paper "Optogenetic identification of striatal projection neuron subtypes during in vivo recordings."
