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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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NEIBank Resource Report Resource Website 10+ mentions |
NEIBank (RRID:SCR_007294) | NEIBank | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | An integrated resource for genomics and bioinformatics in vision research including expressed sequence tag (EST) data and sequence-verified cDNA clones for multiple eye tissues of several species, web-based access to human eye-specific SAGE data through EyeSAGE, and comprehensive, annotated databases of known human eye disease genes and candidate disease gene loci. All expression- and disease-related data are integrated in EyeBrowse, an eye-centric genome browser. NEIBank provides a comprehensive overview of current knowledge of the transcriptional repertoires of eye tissues and their relation to pathology. The data can be interrogated in several ways. Specific gene names can be entered into the search window. Alternatively, regions of the genome can be displayed. For example, entering two STS markers separated by a semicolon (e.g. RH18061;RH80175) allows the display of the entire chromosomal region associated with the mapping of a specific disease locus. ESTs for each tissue can then be displayed to help in the selection of candidate genes. In addition, sequences can be entered into a BLAST search and rapidly aligned on the genome, again showing eye derived ESTs for the same region. To see the same region at the full UCSC site, cut and paste the location from the position window of the genome browser. EyeBrowse includes a custom track display SAGE data for human eye tissues derived from the EyeSAGE project. The track shows the normalized sum of SAGE tag counts from all published eye-related SAGE datasets centered on the position of each identifiable Unigene cluster. This indicates relative activity of each gene locus in eye. Clicking on the vertical count bar for a particular location will bring up a display listing gene details and linking to specific SAGE counts for each eye SAGE library and comparisons with normalized sums for neural and non-neural tissues. To view or alter settings for the EyeSAGE track on EyeBrowse, click on the vertical gray bar at the left of the display. Other custom tracks display known eye disease genes and mapped intervals for candidate loci for retinal disease, cataract, myopia and cornea disease. These link back to further information at NEIBank. | ear, taste, genetics, cdna, chicken, ciliary body, cornea, fovea, dog, guinea pig, human, iris, lacrimal gland, lens, mouse, ocular surface system, optic nerve, rabbit, rat, retina, rpe, choroid, sequence data, trabecular meshwork, whole eye, zebrafish, library, vision, eye, gene, library, disease, loci, ocular genomics, cdna library, expressed sequence tag, blast, cataract, cornea, glaucoma, myopia, retinal disease, genomics, eye tracking device | has parent organization: National Eye Institute (NEI) Commons | Eye disease, Cataract, Glaucoma, Myopia, Retinal disease | NIH Blueprint for Neuroscience Research ; NEI R01 EY13315; NEI R01 EY11286; NEI P30EY0054722 |
PMID:18648525 | nif-0000-00097 | SCR_007294 | NEI Bank | 2026-09-05 06:30:01 | 15 | |||||
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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 | 2026-09-05 06:31:41 | 12 | ||||||
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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 | 2026-09-05 06:31:41 | 10 | |||||
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Gene Array Analyzer Resource Report Resource Website 1+ mentions |
Gene Array Analyzer (RRID:SCR_008323) | GAA | analysis service resource, data analysis service, production service resource, service resource | Data analysis service that allows to process CEL files from Affymetrix, Inc. GeneChip Gene 1.0 ST Arrays to identify alternative splicing. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:22123740 | Acknowledgement requested | OMICS_00759, biotools:gene_array_analyzer | https://bio.tools/gene_array_analyzer | SCR_008323 | 2026-09-05 06:31:52 | 5 | ||||||
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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 | biomaterial supply resource, material resource, tissue bank | 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 | 2026-09-05 06:31:58 | 1 | ||||||
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One Mind Biospecimen Bank Listing Resource Report Resource Website |
One Mind Biospecimen Bank Listing (RRID:SCR_004193) | One Mind Biobanks, One Mind Biobank | biomaterial supply resource, cell repository, material resource | International registry of biomaterial supply resources both for transplantation and research. Contributions to this resource are welcome. The database is searchable through NIF and is updated regularly. | biorepository, bio-repository, database, registry, biobank, biospecimen, repository |
is used by: NIF Data Federation is used by: Aging Portal lists: Midwest Transplant Network lists: Danish Multiple Sclerosis Biobank lists: Genetics of Kidneys in Diabetes lists: TEDDY lists: BioEden Tooth Cell Bank lists: Windber Tissue Bank lists: Boston University Alzheimer's Disease Center Neuropathology Core Facility lists: UCL Biobank lists: LifeLegacy Foundation lists: CCLG Tissue Bank lists: ADA GENNID Study lists: Ohio State Leukemia Tissue Bank lists: Feinstein Biorepository lists: Iowa Donor Network lists: National Disease Research Interchange lists: Emory ADRC Tissue and Biospecimen Banking Facility lists: Zebrafish Brain Atlas lists: KI Biobank - Amphetamine dependence lists: KI Biobank - PAIN lists: PRACSIS - Prognosis and Risk in Acute Coronary Syndromes In Sweden lists: Africa Centre Biobank lists: UCSF Brain Tumor Tissue Bank lists: Southampton Tumour Bank lists: California National Primate Research Center Analytical and Resource Core lists: CPCTR: Cooperative Prostate Cancer Tissue Resource lists: DIAN - Dominantly Inherited Alzheimer Network lists: ZCre lists: Mexican Health and Aging Study lists: NIDDK Inflammatory Bowel Disease Genetics Consortium lists: Acute Liver Failure Study Group lists: Diabetes Prevention Type 1 lists: NIA Mouse cDNA Project Home Page lists: Type 1 Diabetes Resource lists: BARI 2D lists: Childhood Liver Disease Research and Education Network lists: EuMMCR lists: Living Biobank lists: Nonalcoholic Steatohepatitis Clinical Research Network lists: Drug-Induced Liver Injury Network lists: HALT-C Trial lists: SEARCH for Diabetes in Youth lists: Viral Resistance to Antiviral Therapy of Chronic Hepatitis C lists: GenitoUrinary Development Molecular Anatomy Project lists: Medical Therapy of Prostatic Symptoms lists: Type 1 Diabetes Genetics Consortium lists: Texas A and M Institute for Genomic Medicine lists: Expression Patterns for C. elegans promoter GFP fusions lists: ATCC lists: Genes to Cognition - Biological Resources lists: TCAG lists: World Federation for Culture Collections lists: Italian Rett Syndrome database lists: Addgene lists: Rat Resource and Research Center lists: National Center for Marine Algae and Microbiota lists: UD Chick EST Project lists: NCI Mouse Repository lists: CGSC lists: International Gene Trap Consortium lists: Honey Bee Brain EST Project lists: Marine Biological Laboratory lists: NBRC lists: FANTOM DB lists: UMMC Center for Psychiatric Neuroscience Labs and Facilities lists: Gene Expression Nervous System Atlas lists: Washington National Primate Research Center lists: Primate Embryo Gene Expression Resource lists: Peromyscus Genetic Stock Center lists: Islet Cell Resource Centers lists: National Natural Toxins Research Center lists: GenomEUtwin lists: Drosophila Genomics Resource Center lists: Human Tissue and Organ for Research Resource (HTORR) lists: Special Mouse Strains Resource lists: New England National Primate Research Center lists: Addiction Research GPCR Assay Bank lists: Mutant Mouse Resource and Research Center lists: Penn Induced Pluripotent Stem Cell Core Facility lists: neuromice lists: EUROpean Saccharomyces Cerevisiae ARchive for Functional Analysis lists: ShARM lists: NIH NeuroBioBank lists: NIH Human Pluripotent Stem Cell Registry lists: Phoenix lists: The Cancer Genome Atlas lists: MUGEN Mouse Database lists: Coriell Cell Repositories lists: RIKEN BioResource Center lists: Pleiades Promoter Project: Genomic Resources Advancing Therapies for Brain Disorders lists: Retinal Degeneration Rat Model Resource lists: Harvard Brain Tissue Resource Center lists: Glioma Molecular Dignostic Initiatives lists: Source BioScience LifeSciences lists: National Mesothelioma Virtual Bank lists: SpecimenCentral.com lists: Arizona Cancer Center Tumor Bank lists: Cryogenic Laboratories, Inc lists: Partners HealthCare Biorepository lists: National Neurological AIDS Bank lists: Mount Sinai Allograft Technologies lists: EuroBioBank lists: NICHD Brain and Tissue Bank for Developmental Disorders lists: Roswell Park Data Bank and BioRepository lists: Hungarian Neurological-Psychiatric Biobank lists: Roslin Cells lists: Vitiligo Biobank lists: NAF Ataxia Tissue Donation lists: HipSci lists: Cellartis lists: KaLy-Cell lists: Lions Eye Institute for Transplant and Research lists: Endocells lists: Leibniz Institute for Prevention Research and Epidemiology Biobank lists: DCI Tissue and Blood Procurement Shared Resource lists: Childhood Leukaemia Cell Bank lists: Cleveland Clinic Genomic Medicine Biorepository lists: Sunnybrook Tumour Bank lists: Massachusetts Human Stem Cell Bank lists: Liverpool Tissue Bank lists: Dr. Donald MacLellan Tissue Bank lists: OneLegacy lists: Arizona Biospecimen Locator lists: ProMPT - Prostate Cancer Mechanisms of Progression and Treatment lists: British Columbia Gynaecologic Tissue Bank lists: Guthy-Jackson Repository for Neuromyelitis Optica lists: Biorepository Alliance of Georgia for Oncology lists: ITOR Biorepository Services lists: Canadian Tumour Repository Network lists: Progeria Cell and Tissue Bank lists: Wright Medical Technology, Inc. lists: Accelerated Cure Project MS Repository lists: Integrated Biobank of Luxembourg lists: International Biologics, LLC lists: Canadian Breast Cancer Foundation Tumor Bank lists: AIDS and Cancer Specimen Resource lists: Canadian Virtual Brain Tumour Bank lists: UAB Comprehensive Cancer Center Tissue Procurement Shared Facility lists: Cancer Research Network of the FRSQ lists: Biobanking and Biomolecular Resources Research Infrastructure (BBMRI) lists: Bangalore Brain Bank lists: Roslin Wellcome Trust Tick Cell Biobank lists: Osiris Therapeutics lists: LifePoint, Inc. lists: American Donor Services lists: Life Alaska Donor Services, Inc. lists: Biobank Graz lists: UCSF DNA Bank lists: Store-a-Tooth Stem Cell Bank lists: UC San Diego Biorepository lists: START Tumor Bank lists: Donor Alliance lists: University of Minnesota Tissue Procurement Facility lists: NEALS Sample Repository lists: South Texas Blood and Tissue Center lists: New Life Generation, Inc. lists: Transplant Services Center lists: Nevada Donor Network, Inc. lists: OECI - Tubafrost: The European Human Frozen Tissue Bank lists: Cincinnati Biobank Core Facility lists: OHSU Biolibrary lists: Ochsner Blood Bank lists: Brown University Rhode Island Biobank Core Facility lists: Myeloma Tissue Bank lists: US Biomax lists: LifeShare Transplant lists: BioStorage Technologies lists: Duke Biobank lists: UAB Alzheimer's Disease Center lists: Duke Biospecimen Repository lists: Center for Organ Recovery and Education - CORE lists: ReproTech, Ltd. lists: Ludwig Boltzman Tumour Bank lists: Lifesharing Tissue Services lists: Donor Network of Arizona lists: Wales Cancer Bank lists: M2Gen Biorepository lists: Medical College of Georgia Tumor Bank lists: Cellular Technology Ltd Cryopreserved PBMC lists: onCore UK lists: Doheny Eye and Tissue Transplant Bank lists: Dana Farber Tissue Bank lists: Karolisnka Biobank lists: Rocky Mountain MS Center Tissue Bank lists: Marshfield Clinic Biobank lists: Mantle Cell Lymphoma Cell Bank lists: Neuroendocrine Tumors Biobank lists: Case Comprehensive Cancer Center Biorepository and Tissue Processing Core Facility lists: Maryland Brain Collection lists: Angioma Alliance DNA/Tissue Bank and Patient Registry lists: Wisconsin International Stem Cell Bank lists: Mid-America Transplant Services lists: Autism Genetic Resource Exchange lists: Moffitt Cancer Center Tissue Core lists: PROCURE Quebec Prostate Cancer Biobank lists: AIDS Malignancy Bank lists: University of Chicago Human Tissue Resource Center Biospecimen Banking lists: UAB SPORE Biorepository Banks lists: Bone Bank Allografts lists: Allograft Innovations, LLC lists: Origene China lists: Louisiana Organ Procurement Agency - LOPA lists: EDAR study: biomarkers for Alzheimer's disease lists: Cooperative Human Tissue Network lists: UMass Cancer Center Tissue and Tumor Bank lists: Crimson Biospecimen Core lists: ScienceCare lists: St. James Hospital Cryobiology Laboratory Stem Cell Facility lists: BrainNet Europe lists: Essential Tremor Centralized Brain Repository lists: South Dakota Lions Eye Bank lists: Estonian Genome Center lists: Cureline Biopathology lists: Stem-Health Hellas Stem Cell Bank lists: LifeTek OrthoBiologics lists: TissueNet lists: Swedish Regional Biobank lists: Cryo-Save lists: National Surgical Adjuvant Breast and Bowel Project Tissue Bank lists: University of Virginia Tissue Culture Facility lists: KORA-gen lists: Swiss Biobank lists: NIGMS Human Genetic Cell Repository lists: NINDS Repository lists: eyeGENE lists: NHGRI Sample Repository for Human Genetic Research lists: Biobank of Hospital Clinic - IDIBAPS lists: Regional Biobank of Central Norway lists: SeraCare Lifesciences: Sample Storage Management and Processing Services lists: NEI-AREDS Genetic Repository lists: COHORT Repository lists: JP McCarthy Cord Stem Cell Bank lists: Michigan Neonatal Biobank lists: SepNet Central Sample Bank lists: LifeLink Tissue Bank lists: SPH Biorepository lists: Cardio-Facio-Cutaneous Syndrome International Biobank lists: DCI Donor Services lists: LifeGift Organ Donation Center lists: Inflammatory Breast Cancer Biobank lists: University of Miami Tissue Bank lists: LifeNet Health of Florida lists: UTHealth BioBank lists: Southwest France Tumour Bank lists: Southern Alberta Organ and Tissue Donation Program lists: Blood and Tissue Center of Central Texas lists: MD Anderson Clone Bank lists: Community Tissue Services - CTS lists: Aurora Healthcare Biorepository lists: Human Biological Data Interchange lists: Bio-Options lists: Cancer Center Tissue Bank - Fudan University lists: British Columbia Tumour Tissue Repository lists: BioReliance Biorepository lists: New York Firefighters Skin Bank lists: GSDS - Golden State Donor Services lists: UK Multiple Sclerosis Tissue Bank lists: UCL/UCLH Biobank for Studying Health and Disease lists: Tumorbank Bern lists: IPBIR - Integrated Primate Biomaterials and Information Resource lists: Stanford Tissue Bank lists: HD Community BioRepository lists: Autism Research Resource lists: Yerkes Collection Non-Human Primate Resource lists: Hollings Cancer Center Tissue Biorepository and Research Pathology Services Shared Resource lists: Washington Regional Transplant Community - WRTC lists: Vanderbilt BioVU lists: Jackson Laboratory lists: Central England Haemato-Oncology Research Biobank lists: Genethon DNA and Cell Bank lists: University of Michigan Biorepository lists: Simons Simplex Collection lists: Gift of Life Donor Program lists: Queen Square Brain Bank lists: SeqWright Biorepository lists: Telethon Network of Genetic Biobanks lists: New York Organ Donor Network - NYODN lists: Wistar Institute Collection at Coriell lists: USIDNET DNA and Cell Repository lists: Brain Bank for Autism lists: Living Legacy Foundation of Maryland lists: Beaumont Hospitals Biobank lists: Central Biomaterial Bank - German Heart Failure Network lists: PXE International Registry and BioBank lists: Southeast Tissue Alliance, Inc. - SETA lists: National Biobank of Finland lists: CDC Cell and DNA Repository lists: ILSbio lists: California Cryobank, Inc. lists: ETEX Corporation lists: Leiomyosarcoma Cell and DNA Repository lists: HIV Biobank lists: Human Reference Genetic Material Repository lists: Hema-Quebec lists: LifeSource lists: National Temporal Bone Pathology Resource Registry lists: Blood Borne Pathogens Laboratory lists: Susan G. Komen Tissue Bank lists: Ohio State Biorepository lists: Alabama Organ Center lists: TRACK TBI Network lists: National Stem Cell Bank lists: Bioreclamation lists: Biobanque de Picardie lists: Ontario Tumour Bank lists: UK Stem Cell Bank lists: Fox Chase Biosample Repository Core Facility lists: Loma Linda University Cancer Center Biospecimen Laboratory lists: Barth Syndrome Biorepository lists: Interpore Cross International lists: Human Tissue Resource Network lists: California Transplant Services lists: National Cancer Institute Biorepositories lists: LifeCenter Organ Donor Network lists: HemaCare Corp. lists: Human Brain and Spinal Fluid Resource Center lists: Brain and Body Donation Program lists: Kings College London Infectious Diseases BioBank lists: Conticabase - European Sarcoma Database and Tumour Bank lists: Upstate New York Transplant Services lists: Donor Services of Indiana lists: Minnesota Liver Tissue Cell Distribution System lists: Research Tissue Repository - University of Connecticut lists: Mount Sinai Biobank lists: Rocky Mountain Tissue Bank lists: LifeCenter Northwest lists: International Histocompatibility Cell and DNA Bank lists: Regional Tissue Bank lists: Northwest Tissue Services lists: Washington University Tissue Bank lists: Capital Biosciences lists: Lawson Brain Tumour Tissue Bank lists: Andalusian Regional Tumour Bank lists: Protein Biotechnologies lists: Brainbow mouse resource at Jackson Labs lists: RTI Donor Services lists: University Andrology Laboratory lists: Cancer Control using Population-based Registries and Biobanks lists: UCSD Experimental Neuropath Laboratory lists: BioRep lists: da Vinci European Biobank lists: Wisconsin Tissue Bank lists: Indiana Organ Procurement Organization - IOPO lists: Quebec Leukemia Cell Bank lists: LifeBanc lists: Alzheimer's and Dementia Resource Center lists: Tayside Tissue Bank lists: Biobank Suisse lists: Florida Brain Bank lists: Erasmus MC Tissue Bank lists: Hackensack University Tissue Bank lists: World BioBank lists: University of Zurich SCRM - Cell-and Tissue Biobank lists: Tumorbank Basel Foundation lists: LifeLink Foundation lists: Gift of Hope Organ and Tissue Donor Network lists: St. Gallen Lung Biopsy Biobank lists: UNOS - United Network for Organ Sharing lists: UCSF AIDS Specimen Bank lists: MD Anderson Pancreas Tissue Bank lists: Kentucky Organ Donor Affiliates (KODA) lists: German Biobank Registry lists: Tennessee Donor Services lists: UC Davis Biorepository lists: MD Anderson Gynecologic Cancer Tissue Bank lists: Alamo Tissue Service, Ltd. lists: NeuroBiobank Munich lists: Brain-Net lists: Duke University Kathleen Price Bryan Brain Bank lists: Fairfax Cryobank lists: Lifeline of Ohio lists: University of Pittsburgh Brain Tissue Donation Program lists: Medical University of Vienna Institute of Neurology lists: NMDS - New Mexico Donor Services lists: South Carolina Biorepository System lists: CryoLife, Inc. lists: Tissue Banks International - TBI lists: NDRI Dorsal Root Ganglia Program lists: University of Texas Tumor Bank lists: Zebrafish International Resource Center lists: RLS Foundation Brain Bank lists: Dementia Brain Bank Research Program lists: St. Louis University Alzheimer's Brain Bank lists: Beta Cell Biology Consortium lists: UMKC Neuroscience Brain Tissue Bank and Research Laboratory lists: Parkinsons UK Brain Bank Duplicate lists: Einstein-Montefiore Institute for Clinical and Translational Research Biorepository lists: University of Rochester Program for Brain Tumors and Spinal Tumors lists: Case Western Reserve Tissue Procurement and Histology Core Facility lists: Human Tissue Resource Network lists: Boston University Biospecimen Archive Research Core lists: Adenoma Polyp Tissue Bank lists: Brown Brain Tissue Resource Center lists: Texas A and M Health Science Center MSC Distribution lists: JAX Cre Repository lists: Jackson Laboratory Neurobiology lists: WaNPRC Pathology and Tissue Program lists: Geisinger Biobank lists: KI Biobank lists: KI Biobank - KOL lists: Cell Line Knowledge Base lists: KI Biobank - SCI lists: Janus Serum Bank lists: KI Biobank - GEMS lists: KI Biobank - TBI lists: KI Biobank - EIMS lists: KI Biobank - IMSE lists: Vector Database lists: KI Biobank - BROAD lists: KI Biobank - SBP lists: KI Biobank STAGE-ADHD lists: KI Biobank - STANLEY lists: KI Biobank - STAR lists: KI Biobank - EuroClot lists: KI Biobank - Economical Behavior lists: CATSS - Child and Adolescent Twin Study in Sweden lists: DOGSS lists: UMAS University Hospital - Biobanks of the Department of Clinical Pathology and Cytology lists: KI Biobank - SATSA lists: FaceBase Biorepository lists: KI Biobank - SALTY lists: KI Biobank - STAGE lists: KI Biobank - TwinGene lists: BIOAIR - BIOmarkers in severe Chronic AIRway Disease lists: KI Biobank - NOAK lists: OLIN - Obstructive Lung disease in Northern Sweden lists: Cancer of the Prostate in Sweden (CAPS) lists: KI Biobank - CEFALO lists: ICAP - Integrated analysis of prostate cancer lists: LIBRO-1: Individualized prediction and prevention of breast cancer lists: KI Biobank - PROCAP lists: SCALE - Scandinavian lymphoma etiology lists: SPSAC - Stockholm PSA Cohort lists: KI Biobank - Tissue Biobank lists: KI Biobank - CEFAM lists: KI Biobank - PAROKRANK lists: KI Biobank - Sodertaljehjartan lists: CreZOO lists: European Mouse Mutant Archive lists: Toronto Centre for Phenogenomics lists: CMMR - Canadian Mouse Mutant Repository lists: NHMRC Australian PhenomeBank lists: Australian Phenomics Network lists: International Mouse Phenotyping Consortium (IMPC) lists: ZMP lists: Sanger Mouse Resources Portal lists: Chimpanzee Biomedical Research Resource lists: Owl Monkey Breeding and Research Resource lists: Squirrel Monkey Breeding and Research Resource lists: Human Developmental Biology Resource lists: MouseBook lists: Ambystoma Genetic Stock Center lists: Chordoma Foundation Biobank lists: Biobank Ireland Trust lists: UCSF Brain Tumor Tissue Bank lists: Bloomington Drosophila Stock Center lists: NIDDK Central Repository lists: VA Biorepository Brain Bank lists: University of Florida DNA and Tissue Bank lists: Wake Forest Cynomolgus Breeding Colony lists: CCUG: Culture Collection; University of Goteborg; Sweden lists: Dictyostelium discoideum genome database lists: Cooperative Human Tissue Network Western Division at Vanderbilt University Medical Center lists: NCI Breast and Colon Cancer Family Registries lists: British Columbia Breast Cancer Tumour Bank lists: Wake Forest Vervet Research Colony lists: NIMH Stem Cell Center lists: Musculoskeletal Transplant Foundation - MTF lists: NIMH Repository and Genomics Resources lists: Peginterferon and Ribavirin for Pediatric Patients with Chronic Hepatitis C lists: Collaborative Studies on Genetics of Alcoholism lists: National Swine Resource and Research Center lists: National Center for Research Resources - Primate Resources lists: Confederation of Cancer Banks lists: zfishbook lists: SIU CADRD Dementia Brain Autopsy Program lists: Allograft Resources lists: AASK Clinical Trial and Cohort Study lists: I3-CRB: Interoperable IT Infrastructure for Biological Resources Centres / Biobanks - France lists: Stanford Center for Narcolepsy lists: Xenopus Gene Collection lists: Mammalian Gene Collection lists: Parkinsons UK Brain Bank lists: Zebrafish Gene Collection lists: Stanley Brain Collection lists: Boston Area Community Health Survey lists: Central New York Eye and Tissue Bank lists: Chromosome 7 Annotation Project lists: New York Brain Bank at Columbia University lists: Deltagen and Lexicon Knockout Mice and Phenotypic Data Resource lists: National Cell Repository for Alzheimer's Disease lists: NIA Aged Rodent Colonies lists: Knockout Mouse Project Repository lists: NINDS/UCLA Repository for Parkinson's Disease Mouse Models lists: Aging Cell Repository lists: Mouse Mutagenesis Center for Developmental Defects lists: National NeuroAIDS Tissue Consortium lists: NIA Nonhuman Primate Tissue Bank lists: National Alzheimer's Coordinating Center lists: NIA Mutant Mouse Aging Colony Handbook lists: JAX Mice: Neural Tube Defects lists: Caenorhabditis Genetics Center lists: Tulane Stem Cell Research and Regenerative Medicine Tissue Culture Core lists: NUgene Project lists: JAX Neuroscience Mutagenesis Facility lists: Hyper Cell Line Database lists: CHARTER - CNS HIV Antiretroviral Therapy Effects Research lists: BayGenomics lists: Alzheimer's Disease Cooperative Study lists: Baboon Research Resouces lists: Rhesus Monkey Breeding and Research lists: Mouse Mutant Resource lists: EMD4Biosciences lists: German Gene Trap Consortium lists: STRIDE Virtual Biospecimen Bank lists: Stanford/VA Aging Clinical Research Center lists: Spanish National Tumour Bank Network lists: Bioserve Global BioRepository lists: Saint-Luc Tumour Bank lists: Virgin Health Bank lists: UM Brain Endowment Bank lists: Manitoba Breast Tumor Bank lists: NIMH Brain Tissue Collection lists: UCL-RFH BioBank lists: Coriell Institute Stem Cell Biobank lists: MassGeneral Institute for Neurodegenerative Disease lists: Mayo Clinic Jacksonville: Neuropathology and Microscopy lists: NYU Alzheimer's Disease Center lists: Brain Research Institute Biobank Resources lists: Johns Hopkins Alzheimer's Disease Research Center lists: Rush Alzheimer's Disease Center lists: Massachusetts Alzheimer's Disease Research Center lists: University of Kentucky's Alzheimer's Disease Center lists: Michigan Alzheimer's Disease Center Brain Bank lists: Washington University Knight Alzheimer's Disease Research Center lists: Mount Sinai Alzheimer's Disease Research Center lists: Taub Institute for Research on Alzheimers Disease and the Aging Brain lists: Institute for Basic Research in Developmental Disabilities lists: Vietnam Era Twin Registry Biospecimen Repository lists: Study of Womens Health Across the Nation (SWAN) Repository lists: Dynamics of Health Aging and Body Composition (Health ABC) lists: University of Pennslyvania Brain Bank lists: Layton Center Biomarkers and Genetics lists: MUSC Center on Aging Campbell Neuropathology Laboratory lists: UT Southwestern ADC Brain Tissue Donation Program lists: KI Biobank - Parkinson lists: KI Biobank - EXT lists: GIA Brain Bank Program lists: KI Biobank - ALF lists: KI Biobank - HARMONY lists: Twin Study of Child and Adolescent Development - TCHAD lists: SHEEP - Stockholm Heart Epidemiology Program lists: CreZoo lists: Fleming Database lists: Los Angeles Family and Neighborhood Survey lists: Health and Retirement Study lists: Iowa 65+ Rural Health Study lists: National Long Term Care Survey lists: National Social Life Health and Aging Project (NSHAP) lists: Framingham Heart Study lists: Integrated Cell Lines lists: Chronic Renal Insufficiency Cohort Study lists: PrecisionMed lists: Biopta lists: Manhattan HIV Brain Bank lists: LifeGene lists: Puget Sound Blood Center lists: Fisher BioServices lists: National Psoriasis BioBank lists: StemCure Tissue Banking lists: ProMedDx lists: Biological Resource Centre - National Institute for Cancer Research lists: Coriell Biobank lists: StemSave lists: Dublin Brain Bank lists: Mayo Mitochondrial Disease Biobank lists: NIA Aged Rodent Tissue Bank lists: MVZ Collections lists: CARTaGENE lists: European Collection of Cell Cultures lists: UK DNA Banking Network lists: Biobanc USA lists: Rutgers Cell and DNA Repository lists: Genetic Alliance Biobank lists: Hunt Biobank lists: Advanced Biohealing, Inc. lists: Edinburgh Brain and Tissue Banks lists: JCM lists: Movement Disorders Biobank lists: Surgical Biologics - a MiMedx Group Company lists: Chernobyl Tissue Bank lists: Tissue Solutions lists: Conversant Biologics Inc. lists: Narayana Hrudayalaya Tissue Bank and Stem Cell Research Center lists: AlloSource lists: PathServe lists: UC Davis Alzheimers Disease Center - Resources lists: Asterand lists: RTI Biologics lists: Mayo Clinic Biobank lists: Lifelines Biobank lists: Mayo Validation Support Services Biobank lists: LifeNet Health lists: Medical Biobank lists: Fraunhofer Institute for Biomedical Engineering lists: BWH Specimen Bank lists: University of Minnesota Bionet - Academic Health Center lists: DF/HCC DNA Resource Core lists: Indiana Alzheimer Disease Center lists: UK Biobank lists: National Institute on Drug Abuse Center for Genetic Studies lists: Oregon Brain Bank lists: Biologic Specimen and Data Repository Information Coordinating Center (BioLINCC) lists: Northwestern CNADC Tissue Bank / Neuropathology Core lists: Loyola University Medical Center / Hines VA Brain Bank lists: Trinity Biobank lists: SAPALDIA lists: Ohio U Diabetes Endocrine Biorepository lists: National Cell Culture Center lists: Diabetic Complications Consortium lists: Xenbase lists: Blueprint Epigenome lists: EBiSC lists: Biospecimens/Biorepositories: Rare Disease-HUB (RD-HUB) lists: Parkinson's Progression Markers Initiative lists: OriGene lists: University of Nottingham NASC Nottingham Arabidopsis Stock Centre is related to: Rat Resource and Research Center is related to: Honey Bee Brain EST Project is related to: Islet Cell Resource Centers is related to: Special Mouse Strains Resource is related to: NIH Human Pluripotent Stem Cell Registry is related to: Harvard Brain Tissue Resource Center is related to: Louisiana Organ Procurement Agency - LOPA is related to: Washington Regional Transplant Community - WRTC is related to: Minnesota Liver Tissue Cell Distribution System is related to: Zebrafish International Resource Center is related to: Bloomington Drosophila Stock Center is related to: National Swine Resource and Research Center is related to: Xenopus Gene Collection is related to: Mammalian Gene Collection is related to: Zebrafish Gene Collection is related to: Mouse Mutagenesis Center for Developmental Defects is related to: NIA Mutant Mouse Aging Colony Handbook is related to: Manhattan HIV Brain Bank is related to: National Institute on Drug Abuse Center for Genetic Studies is related to: International Mouse Strain Resource is related to: Jackson Laboratory is related to: Rat Genome Database (RGD) is related to: VISTA Enhancer Browser is related to: GenitoUrinary Development Molecular Anatomy Project is related to: Coriell Cell Repositories is related to: NICHD Brain and Tissue Bank for Developmental Disorders is related to: Human Brain and Spinal Fluid Resource Center is related to: UM Brain Endowment Bank has parent organization: One Mind for Research has parent organization: Neuroscience Information Framework |
The community can contribute to this resource, Data are licensed by their respective owners, Use and distribution is subject to the Terms of Use by the original resource | nlx_143622 | https://neuinfo.org/mynif/search.php?q=*&cf=Biospecimen&t=indexable&nif=nlx_143622-1 http://neuinfo.org/onemind/index.php?q=*&b=0&r=20 | SCR_004193 | One Mind: One Voice Bio-repository Cosmic Landscape, One Mind Biospecimen Banks | 2026-09-05 06:30:39 | 0 | ||||||
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Mammalian Gene Collection Resource Report Resource Website 10+ mentions |
Mammalian Gene Collection (RRID:SCR_007024) | MGC | biomaterial supply resource, cell repository, material resource | NIH initiative project to provide full-length open reading frame (FL-ORF) clones for human, mouse, and rat genes, cow. MGC cDNA clones were obtained by screening of cDNA libraries, by transcript-specific RT-PCR cloning, and by DNA synthesis of cDNA inserts. All MGC sequences are deposited in GenBank and clones can be purchased from distributors of IMAGE consortium. With conclusion of MGC project in March 2009, GenBank records of MGC sequences will be frozen, without further updates. Since definition of what constitutes full-length coding region for some of genes and transcripts for which they have MGC clones will likely change in future, users planning to order MGC clones will need to monitor for these changes. Users can make use of genome browsers and gene-specific databases, such as the UCSC Genome browser, NCBI's Map Viewer, and Entrez Gene, to view relevant regions of genome (browsers) or gene-related information (Entrez Gene). | cell line, cdna, frozen, clone, vector, gene, open reading frame, sequence, expressed sequence tag, bio.tools, FASEB list |
is listed by: One Mind Biospecimen Bank Listing is listed by: bio.tools is listed by: Debian is related to: One Mind Biospecimen Bank Listing is related to: NIDDK Information Network (dkNET) is related to: ATCC is related to: GenBank is related to: Invitrogen Clones is related to: Open Biosystems is related to: Zebrafish Gene Collection has parent organization: National Cancer Institute |
NIH Blueprint for Neuroscience Research | Free, Freely available | biotools:mammalian_gene_collection, nif-0000-00195 | https://bio.tools/mammalian_gene_collection | SCR_007024 | Mammalian Gene Collection | 2026-09-05 06:30:42 | 46 | |||||
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Rat Brain Atlas of Paxinos and Watson Resource Report Resource Website 10+ mentions |
Rat Brain Atlas of Paxinos and Watson (RRID:SCR_006369) | Rat Brain Atlas of Paxinos & Watson | atlas, data or information resource, reference atlas | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 27,2025. Compact 3rd edition of The Rat Brain Atlas of Paxinos & Watson published in 1997, it is the most widely used stereotaxic reference system for rat brain. The illustrations and nomenclature of the atlas have become standard tools used by almost all research neuroscientists who deal with anatomy, physiology, or function. It has been subsequently updated, with the 6th edition being the most recent. The 3rd edition is the most recent one available online for free. The program runs in Adobe Acrobat Reader. | rat, stereotaxic coordinate, brain, neuroanatomy | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_152120 | SCR_006369 | Rat Brain Atlas - Paxinos & Watson, Rat Brain in Stereotaxic Coordinates | 2026-09-05 06:30:42 | 20 | ||||||||
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3D DTI Atlas of the Rat Brain In Postnatal Day 5 14 and Adulthood Resource Report Resource Website 1+ mentions |
3D DTI Atlas of the Rat Brain In Postnatal Day 5 14 and Adulthood (RRID:SCR_009437) | 3D DTI Atlas of the Rat Brain | atlas, data or information resource, reference atlas | 3D DTI anatomical rat brain atlases have been created by the UNC- Chapel Hill Department of Psychiatry and the CAMID research collaboration. There are three age groups, postnatal day 5, postnatal day 14, and postnatal day 72. The subjects were Sprague-Dawley rats that were controls in a study on cocaine abuse and development. The P5 and P14 templates were made from scans of twenty rats each (ten female, ten male); the P72, from six females. The individual cases have been resampled to isotropic resolution, manually skull-stripped, and deformably registered via an unbiased atlas building method to create a template for each age group. Each template was then manually segmented using itk-SNAP software. Each atlas is made up of 3 files, a template image, a segmentation, and a label file. | magnetic resonance, adult rat, newborn rat, infant rat, young rat, sprague dawley, male, female |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
Control, Normal | UNC Neurodevelopment Disorders Research Center ; NICHD HD 03110; NINDS R41 NS059095; NIDA IP01DA022446-02 |
nlx_155577 | SCR_009437 | 3-Dimensional Diffusion Tensor Imaging (DTI) Atlas of the Rat Brain In Postnatal Day 5 14 and Adulthood | 2026-09-05 06:30:45 | 2 | ||||||
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HomoloGene Resource Report Resource Website 100+ mentions |
HomoloGene (RRID:SCR_002924) | HomoloGene | data or information resource, database, service resource | Automated system for constructing putative homology groups from complete gene sets of wide range of eukaryotic species. Databse that provides system for automatic detection of homologs, including paralogs and orthologs, among annotated genes of sequenced eukaryotic genomes. HomoloGene processing uses proteins from input organisms to compare and sequence homologs, mapping back to corresponding DNA sequences. Reports include homology and phenotype information drawn from Online Mendelian Inheritance in Man, Mouse Genome Informatics, Zebrafish Information Network, Saccharomyces Genome Database and FlyBase. | homolog, paralog, ortholog, genome, gene, protein, protein alignment, phenotype, conserved domain, homology, amino acid sequence, cell, dna, gold standard |
is used by: NIF Data Federation is used by: Nowomics is used by: MitoMiner is listed by: OMICtools is listed by: re3data.org is related to: OMIM is related to: Mouse Genome Informatics (MGI) is related to: Zebrafish Information Network (ZFIN) is related to: SGD is related to: FlyBase is related to: ProbeMatchDB 2.0 is related to: Biomine is related to: Consensus CDS has parent organization: NCBI |
PMID:23193264 | Free, Freely availalbe | nif-0000-02975, r3d100010781, OMICS_01544 | http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=homologene, https://doi.org/10.17616/R3889F | SCR_002924 | NCBI HomoloGene | 2026-09-05 06:31:19 | 459 | |||||
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Knowledgebase for Addiction Related Genes Resource Report Resource Website 1+ mentions |
Knowledgebase for Addiction Related Genes (RRID:SCR_002687) | KARG | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. Database of data and knowledge linking genes and chromosome regions to addiction that were extracted from reviewing more than 1,000 peer-reviewed publications from between 1976 and 2006. This list of publications included review papers on addiction selected from results of PUBMED query "(addiction OR drug abuse) AND review" as well as research papers selected from PUBMED query "(addiction OR drug abuse) AND (gene OR microarray OR proteomics OR QTL OR population association OR genetic linkage)". The data spanned multiple technology platforms including classical hypothesis-testing of single genes, identification of significantly differentially expressed genes in microarray experiments, identification of significantly differentially expressed proteins in proteomics assays, identification of addiction-vulnerable chromosome regions in animal QTL studies, genetic linkage studies, population association studies, and OMIM annotations. From each publication they collected the genes, proteins, or chromosome regions linked to addiction, as well as metadata such as species, nature of the addictive substance, studied brain regions, technology platforms, and experimental parameters. In total, they collected 2,343 items of evidence linking 1,500 human genes to addiction. Among them 396 genes were supported by two or more items of evidence. The interface supports browsing of the genes by chromosome or pathways, advanced text search by gene ID, organism, type of addictive substance, technology platform, protein domain, and/or PUBMED ID, and sequence search by BLAST similarity. All data, database schema, and MySQL commands are freely available for download. | molecular neuroanatomy resource, gwas, meta-analysis, genetic susceptibility, gene, protein, chromosome, pathway, drug of abuse, blast, addiction, substance abuse, drug abuse, microarray, proteomics, qtl, population association, genetic linkage |
uses: PubMed has parent organization: Peking University; Beijing; China |
PMID:18179280 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00411 | SCR_002687 | KARG: Knowledgebase for Addiction-Related Gene, Knowledgebase for Addiction-Related Gene, KARG: Knowledgebase for Addiction Related Genes | 2026-09-05 06:31:18 | 8 | ||||||
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ABS: A Database of Annotated Regulatory Binding Sites From Orthologous Promoters Resource Report Resource Website 1+ mentions |
ABS: A Database of Annotated Regulatory Binding Sites From Orthologous Promoters (RRID:SCR_002276) | ABS | data or information resource, database | Public database of known binding sites identified in promoters of orthologous vertebrate genes that have been manually curated from bibliography. We have annotated 650 experimental binding sites from 68 transcription factors and 100 orthologous target genes in human, mouse, rat or chicken genome sequences. Computational predictions and promoter alignment information are also provided for each entry. For each gene, TFBSs conserved in orthologous sequences from at least two different species must be available. Promoter sequences as well as the original GenBank or RefSeq entries are additionally supplied in case of future identification conflicts. The final TSS annotation has been refined using the database dbTSS. Up to this release, 500 bps upstream the annotated transcription start site (TSS) according to REFSEQ annotations have been always extracted to form the collection of promoter sequences from human, mouse, rat and chicken. For each regulatory site, the position, the motif and the sequence in which the site is present are available in a simple format. Cross-references to EntrezGene, PubMed and RefSeq are also provided for each annotation. Apart from the experimental promoter annotations, predictions by popular collections of weight matrices are also provided for each promoter sequence. In addition, global and local alignments and graphical dotplots are also available. | gene, alignment, annotation, binding, computational, genome, nucleotide, ortholog, prediction, promoter, sequence, target, transcription, transcriptional factor, binding site, promoter sequence, protein motif, benchmark, transcription factor binding site, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: IntegromeDB has parent organization: Center for Genomic Regulation; Barcelona; Spain |
European Union FP6 contract LSHG-CT-2003-503265 | PMID:16381947 | Acknowledgement requested, GNU General Public License, v2 | biotools:alggen, nif-0000-21006 | https://bio.tools/alggen | SCR_002276 | A database of Annotated regulatory Binding Sites from orthologous promoters | 2026-09-05 06:31:17 | 3 | ||||
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DOMINO: Domain peptide interactions Resource Report Resource Website 50+ mentions |
DOMINO: Domain peptide interactions (RRID:SCR_002392) | data or information resource, database | Open-access database comprising more than 3900 annotated experiments describing interactions mediated by protein-interaction domains. The curation effort aims at covering the interactions mediated by the following domains (SH3, SH2, 14-3-3, PDZ, PTB, WW, EVH, VHS, FHA, EH, FF, BRCT, Bromo, Chromo, GYF). The interactions deposited in DOMINO are annotated according to the PSI MI standard and can be easily analyzed in the context of the global protein interaction network as downloaded from major interaction databases like MINT, INTACT, DIP, MIPS/MPACT. It can be searched with a versatile search tool and the interaction networks can be visualized with a convenient graphic display applet that explicitly identifies the domains/sites involved in the interactions. | annotation, protein interaction, protein-interaction domain, sh3, sh2, pdz, 14-3-3, ww |
is listed by: OMICtools is related to: PSI-MI has parent organization: University of Rome Tor Vergata; Rome; Italy |
PMID:17135199 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01907, nif-0000-02759, r3d100010684 | https://doi.org/10.17616/R3K32V | SCR_002392 | DOMINO | 2026-09-05 06:31:17 | 53 | ||||||
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DBTSS: Database of Transcriptional Start Sites Resource Report Resource Website 100+ mentions |
DBTSS: Database of Transcriptional Start Sites (RRID:SCR_002354) | DBTSS | data or information resource, database | Database of transcriptional start sites (TSSs) representing exact positions in the genome based on a unique experimentally validated TSS sequencing method, TSS Seq. A major part of human adult and embryonic tissues are covered. DBTSS contains 491 million TSS tag sequences collected from a total of 20 tissues and 7 cell cultures. Also integrated is generated RNA-seq data of subcellular- fractionated RNAs and ChIP Seq data of histone modifications, RNA polymerase II and several transcriptional regulatory factors in cultured cell lines. Also included is external epigenomic data, such as chromatin map of the ENCODE project. They associated those TSS information with public and original SNV data, in order to identify single nucleotide variations (SNVs) in the regulatory regions. | cdna, cdna library, transcriptional start site, transcriptome, transcriptome analysis, tss-seq, genome, adult human, embryonic, cell, rna-seq, subcellular, rna, chip seq data, histone modification, rna polymerase ii, transcriptional regulatory factor, cell line, single nucleotide variation, regulatory region, genetic valuation, transcriptional regulation, bio.tools, FASEB list |
is used by: Transcriptional Regulatory Element Database is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Tokyo; Tokyo; Japan |
Japan Society for the Promotion of Science ; Japanese Ministry of Education Culture Sports Science and Technology MEXT |
PMID:22086958 PMID:19910371 PMID:17942421 PMID:16381981 PMID:14681363 PMID:11752328 |
nif-0000-02738, biotools:dbtss, OMICS_01860 | https://bio.tools/dbtss | SCR_002354 | DBTSS: Database of Transcriptional Start Sites, DataBase of Transcriptional Start Sites | 2026-09-05 06:31:17 | 127 | |||||
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MapViewer Resource Report Resource Website 100+ mentions |
MapViewer (RRID:SCR_003092) | Map Viewer | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4, 2023. Database that provides special browsing capabilities for a subset of organisms in Entrez Genomes. Map Viewer allows users to view and search an organism's complete genome, display chromosome maps, and zoom into progressively greater levels of detail, down to the sequence data for a region of interest. If multiple maps are available for a chromosome, it displays them aligned to each other based on shared marker and gene names, and, for the sequence maps, based on a common sequence coordinate system. | genome, mapping, sequencing, chromosome |
is listed by: OMICtools is related to: NCBI Genome is related to: Consensus CDS has parent organization: NCBI |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00921, nif-0000-03103 | SCR_003092 | Entrez Map Viewer, NCBI Map Viewer | 2026-09-05 06:31:19 | 244 | |||||||
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Schramm Lab Spinal Cord Atlases Resource Report Resource Website |
Schramm Lab Spinal Cord Atlases (RRID:SCR_003265) | Schramm Lab Spinal Cord Atlases | atlas, data or information resource | Serial histological sections of rat spinal cord at the lumbar and thoracic levels. Serial sections of rat spinal cord cut in the horizontal and sagittal planes. Also transverse and sagittal section series of the postnatal thoracic spinal cord immunolabeled for SMI-32. | histological section, lumbar spinal cord, rat, serial tissue section, thoracic spinal cord, spinal cord, lumbar, horizontal, sagittal, postnatal, transverse | has parent organization: Johns Hopkins University; Maryland; USA | Free, Freely available | nif-0000-00021 | SCR_003265 | 2026-09-05 06:31:20 | 0 | ||||||||
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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 | 2026-09-05 06:31:20 | 2 | |||||
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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 | atlas, data or information resource, waxholm 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 |
EC Human Brain Project ; NCI U24 CA092656; NIBIB P41 EB015897; Research Council of Norway |
PMID:24726336 PMID:25585022 |
Free, Available for download, Freely available | SCR_017124 | WHS SD rat atlas, WHS_SD_rat_atlas, WHS-SD-rat-atlas | 2026-09-05 06:32:14 | 38 | ||||||
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FuncAssociate: The Gene Set Functionator Resource Report Resource Website 10+ mentions |
FuncAssociate: The Gene Set Functionator (RRID:SCR_005768) | FuncAssociate | analysis service resource, data analysis service, production service resource, service resource | A web-based tool that accepts as input a list of genes, and returns a list of GO attributes that are over- (or under-) represented among the genes in the input list. Only those over- (or under-) representations that are statistically significant, after correcting for multiple hypotheses testing, are reported. Currently 37 organisms are supported. In addition to the input list of genes, users may specify a) whether this list should be regarded as ordered or unordered; b) the universe of genes to be considered by FuncAssociate; c) whether to report over-, or under-represented attributes, or both; and d) the p-value cutoff. A new version of FuncAssociate supports a wider range of naming schemes for input genes, and uses more frequently updated GO associations. However, some features of the original version, such as sorting by LOD or the option to see the gene-attribute table, are not yet implemented. Platform: Online tool | gene, gene ontology, statistical analysis, web service, bio.tools |
is listed by: Gene Ontology Tools is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Gene Ontology has parent organization: Roth Laboratory |
NIH ; Canadian Institute for Advanced Research ; NINDS NS054052; NINDS NS035611; NHLBI HL081341; NHGRI HG0017115; NHGRI HG004233; NHGRI HG003224 |
PMID:19717575 PMID:14668247 |
Free for academic use, Acknowledgement requested | biotools:funcassociate, OMICS_02264, nlx_149233 | http://llama.mshri.on.ca/cgi/func/funcassociate, https://bio.tools/funcassociate | SCR_005768 | 2026-09-05 06:31:31 | 36 | |||||
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ADGO Resource Report Resource Website 1+ mentions |
ADGO (RRID:SCR_006343) | ADGO | analysis service resource, data analysis service, production service resource, service resource | A web-based tool that provides composite interpretations for microarray data comparing two sample groups as well as lists of genes from diverse sources of biological information. It provides multiple gene set analysis methods for microarray inputs as well as enrichment analyses for lists of genes. It screens redundant composite annotations when generating and prioritizing them. It also incorporates union and subtracted sets as well as intersection sets. Users can upload their gene sets (e.g. predicted miRNA targets) to generate and analyze new composite sets. | microarray, gene, annotation, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:21624890 | Acknowledgement requested | OMICS_02229, biotools:adgo | https://bio.tools/adgo | SCR_006343 | 2026-09-05 06:31:34 | 3 |
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