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

(last updated: Oct 12, 2019)

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Resource NameResource TypeDescriptionKeywordsResource IDProper CitationParent OrganizationRelated ConditionFunding AgencyRelationReferenceWebsite StatusAlternate IDsAlternate URLsOld URLs
Drug-Induced Liver Injury Network Resource, disease-related portal, topical portal, resource, research forum portal, biomaterial supply resource, people resource, bibliography, portal, patient registry, material resource, clinical trial, data or information resourceProspective and retrospective registry of well-characterized cases of drug-induced liver disease. The goals of Network include the development of standardized procedures to identify and fully characterize bona fide cases of drug- and complementary and alternative medicines (CAM)-induced liver injury, and to conduct controlled, clinical studies that will include extensive collection of data, serum, DNA, and tissue specimens. Cases of liver injury due to herbal medications are also included. The network will also develop terminology and standardized definitions for DILI, and to develop causality assessment instruments that are sensitive, specific, and reproducible. DILIN is funded by a cooperative agreement and includes five clinical centers and a central data coordinating center. The research goals of DILIN are to: * Create a registry of carefully documented DILI cases * Identify clinical, immunological, and environmental risk factors for drug- and CAM-mediated hepatotoxicity * Create a bank of biological specimens consisting of DNA, plasma, and immortalized lymphocytes to facilitate detailed genetic analyses * Characterize the natural history of drug- and CAM-induced DILI for at least six months following enrollment * Develop the capability to recontact these individuals over an extended period of time so that additional studies exploring DILI mechanisms can be performed Two studies are being initiated by the network. In the Retrospective Study, the implicated drugs are restricted to isoniazid, phenytoin, combination clavulanic acid/amoxicillin, and valproic acid (Depakote), Nitrofurantoin, Trimethoprim-sulfamethoxazole, Minocycline, and Quinolone antibiotics. These drugs were chosen because they are frequently administered to patients not receiving other hepatotoxic drugs, making it easier to establish causality. Patients must be alive, and the date of onset of the DILI episode must be on or after January 1, 1994. In the Prospective Study, all incident cases of drug- and CAM-induced liver injury are being considered. Initial presentation to a healthcare professional must be within the previous six months. A detailed medication history of the implicated DILI drug together with all prescription, OTC, and herbal medications is being recorded. Liver and serological tests are being performed to characterize the injury and to exclude competing causes of liver injury. A blood sample is also being drawn for plasma storage and DNA isolation. These cases will be followed longitudinally to characterize the long-term effects of the DILI episode. For both studies, documented, clinically significant DILI must be recorded in the patient's medical charts so that a causal determination can be made. Patients will be excluded if they are unwilling or unable to provide a blood sample or participate in the genetics component. Children under two years of age at the time of enrollment are excluded due to blood-volume requirements. If you have patients who are eligible to participate in either study, please contact one the DILIN clinical sites. As a general policy, the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) invites investigator-initiated research project applications for ancillary studies to ongoing, large-scale clinical trials, epidemiological studies, and disease databases supported by the Institute. These studies are focused on a wide range of diseases and conditions including diabetes, obesity, acute and chronic liver disease, chronic kidney disease, and benign prostatic hyperplasia, among others.prescription drug, over-the-counter drug, alternative medicine, herbal product, supplement, serum, dna, tissue, blood, immortalized lymphocyte, drug, medication, quinolone antibiotic, isoniazid, phenytoin, clavulanic acid, amoxicillin, valproic acid, depakote, nitrofurantoin, trimethoprim-sulfamethoxazole, minocycline, diagnosis, hepatotoxicity, risk factor, genetic analysisSCR_001524( Drug-Induced Liver Injury Network , RRID:SCR_001524)Duke University; North Carolina; USA Liver injury, Hepatic injury, Drug-induced liver diseaseNIDDKlisted by: One Mind Biospecimen Bank Listing, NIDDK Information Network, Diabetes Research Centers, submitted by: NIDDK Information NetworkLast checked downnlx_152822
University of Leeds - Computational Biology GroupResource, topical portal, portal, data or information resourceThe University of Leeds Computational Biology Group is an interdisciplinary research group based in the Faculty of Biological Sciences, and is part of the Centre for Nonlinear Studies. Research interests are at the interfaces of nonlinear dynamics, computational science and general physiology of excitable tissue (nervous system, cardiac and uterine muscle). A central theme is the reconstruction of tissue and organ physiology and pathologies from networks of intracellular, membrane and cellular models. Sponsors:biological science, cardiac muscle, cellular model, computational biology, intracellular model, membrane model, nervous system, nonliear study, organ, pathology, physiology, tissue, uterine muscleSCR_001956(University of Leeds - Computational Biology Group, RRID:SCR_001956)Last checked downnif-0000-10528http://www.cbiol.leeds.ac.uk/
Biobanking and Biomolecular Resources Research Infrastructure (BBMRI)Resource, topical portal, database, biomaterial supply resource, portal, material resource, data or information resourceBBMRI is a pan-European and internationally broadly accessible research infrastructure and a network of existing and de novo biobanks and biomolecular resources. The infrastructure will include samples from patients and healthy persons, representing different European populations (with links to epidemiological and health care information), molecular genomic resources and biocomputational tools to optimally exploit this resource for global biomedical research. During the past 3 years BBMRI has grown into a 53-member consortium with over 280 associated organizations (largely biobanks) from over 30 countries, making it the largest research infrastructure project in Europe. During the preparatory phase the concept of a functional pan-European biobank was formulated and has now been presented to Member States of the European Union and for associated states for approval and funding. BBMRI will form an interface between specimens and data (from patients and European populations) and top-level biological and medical research. This can only be achieved through a distributed research infrastructure with operational units in all participating Member States. BBMRI will be implemented under the ERIC (European Research Infrastructure Consortium) legal entity. BBMRI-ERIC foresees headquarters (central coordination) in Graz, Austria, responsible for coordination of the activities of National Nodes established in participating countries. BBMRI is in the process of submitting its application to the European Commission for a legal status under the ERIC regulation, with an expected start date at the end of 2011. Major synergism, gain of statistical power and economy of scale will be achieved by interlinking, standardizing and harmonizing - sometimes even just cross-referencing - a large variety of well-qualified, up-to date, existing and de novo national resources. The network should cover (1) major European biobanks with blood, serum, tissue or other biological samples, (2) molecular methods resource centers for human and model organisms of biomedical relevance, (3) and biocomputing centers to ensure that databases of samples in the repositories are dynamically linked to existing databases and to scientific literature as well as to statistical expertise. Catalog of European Biobanks www.bbmriportal.eu Username: guest / Password: catalogue The catalogue is intended to be used as a reference for scientists seeking information about biological samples and data suitable for their research. The BBMRI catalogue of European Biobanks provides a high-level description of Europe''s biobanks characteristics using a portal solution managing metadata and aggregate data of biobanks. The catalogue can be queried by country, by biobank, by ICD-groups, by specimen types, by specific strengths, by funding and more. A search function is available for all data.blood, serum, tissue, dna, cdna, rna, plasma, cell line, bodily fluid, urine, blood cell isolate, buffy coat, patient, healthy, normal, cryopreserved, paraffin embedded, clinical dataSCR_004226(Biobanking and Biomolecular Resources Research Infrastructure (BBMRI), RRID:SCR_004226)Medical University of Graz; Graz; Austria All, Patient, Healthy, NormalEuropean Unionrelated to: BioResource Impact Factor, German Biobank Registry, BioMedBridges, Biological Resource Centre - National Institute for Cancer Research, listed by: One Mind Biospecimen Bank ListingLast checked downnlx_24389http://www.bbmri.eu/index.php
University of Rochester Program for Brain Tumors and Spinal TumorsResource, topical portal, biomaterial supply resource, tissue bank, portal, brain bank, material resource, data or information resourceCollaborative neuro-oncology research program with a tissue repository (tumor bank) containing a wide range of clinical specimens, which they make available to researchers in order to study the effects of new drugs on a large number and wide range of tumor specimens. They provide highly coordinated, complex care in neurosurgery, radiation oncology, medical oncology, and neurology to patients afflicted with tumors of the brain and spine by combining the newest technologies and treatments available anywhere in the world. The program is formed from a multidisciplinary group with a goal of helping patients navigate the complex issues surrounding brain and spinal cancer care. The researchers are working to increase the number of targets that could be considered for anti-angiogenesis therapy. Many of their studies focus on the blood vessel cells (endothelial cells) themselves, which, unlike tumor cells, rarely mutate and so might be less likely to become resistant to therapy and are also more easily reached through the bloodstream. Their researchers are also attempting to better understand the changes in the blood-brain barrier (BBB) that are associated with fluid accumulation and brain swelling (edema) in neuro-oncology patients. Normal brain tissue is shielded from the rest of the body by the BBB. This barrier is composed of very tight blood vessels that prevent most substances from entering the brain. Brain tumors have a leaky BBB ?????? this feature can be used to identify tumors on MRI scans. They have identified specific molecules that appear to be associated with the leaky, abnormal vessels while the normal blood vessels with intact BBB produce these molecules at very low levels or not at all. Inhibiting the function of these molecules may help control or prevent disruption of the BBB and limit cerebral edema in brain tumor patients, as well as patients suffering from stroke or traumatic brain injury.brain tissue, brain, tissue, spine, spinal tumor, brain tumor, tumor, cancer, normal control, clinical trial, treatment, acoustic neuroma, anaplastic astrocytoma, brain metastases, brain stem glioma, chordoma, cns lymphoma, craniopharyngioma, ependymoma, gliomatosis cerebri, glioblastoma, low grade glioma, meningioma, medulloblastoma, oligodendroglioma, pineal tumor, pilocytic astrocytoma, pituitary adenoma, premature neuroectodermal tumor, oncology, neurooncology, stroke, traumatic brain injury, cerebral edemaSCR_005343(University of Rochester Program for Brain Tumors and Spinal Tumors, RRID:SCR_005343)Tumor, Brain tumor, Cancer, Spinal tumor, Normal controllisted by: One Mind Biospecimen Bank ListingLast checked downnlx_144398http://www.urmc.rochester.edu/neurosurgery/neurooncology/overview/research/
I3-CRB: Interoperable IT Infrastructure for Biological Resources Centres / Biobanks - FranceResource, topical portal, biomaterial supply resource, data set, portal, material resource, data or information resourceProject to improve data and sample exchanges and to facilitate large scale analysis of data by improving interoperability of French Biological Resources Centres (BRC or biobanks) IT systems and biological databases. The work done in this project will be linked to other national (IBiSA, ANR, R??seau des Biobanques, Club 3C-R), European (BBMRI, ELIXIR) or international project (P3G). In the preliminary phase (2009-2010) I3-CRB has developed a directory of French Biological Resource Centres / Biobanks where one may register their French BRC or perform a search across all of them. Detail by overall data or kingdom is provided as well as many filtering options. Access to biological samples is provided by the participating BRC''''s. Biological Resources Centres (BRC or biobanks) collect annotated biological samples from various sources (human, animal, plant, bacteria...). The type of samples depends on the collection and the associated thematic (DNA, proteins, cells, tissues, blood, serum, organisms...). The aims of these centers are to collect, to store, to transform and to distribute the biological samples. They constitute a vital infrastructure for life science and health research. Goals of the French Biobanks/Biological Resource Centres: * List French biobanks and their biological collections * Improve sample exchanges * Improve the international visibility of the French biological collections MeSH terms have been integrated: Domains, diseases, and location of the disease (Anatomy). Collections/species are based on NCBI Taxonomy.plant, animal, human, micro-organism, microorganism, bacteria, dna, protein, cell, tissue, blood, serum, organism, researchSCR_006991(I3-CRB: Interoperable IT Infrastructure for Biological Resources Centres / Biobanks - France, RRID:SCR_006991)University Lyon; Lyon; France GIS IBiSArelated to: MeSH, listed by: One Mind Biospecimen Bank ListingLast checked downnlx_36068
Stanford Center for NarcolepsyResource, topical portal, biomaterial supply resource, tissue bank, service resource, brain bank, storage service resource, portal, material storage repository, material resource, video resource, data or information resourceThe Stanford Center for Narcolepsy was established in the 1980s as part of the Department of Psychiatry and Behavioral Sciences. Today, it is the world leader in narcolepsy research with more than 100 articles on narcolepsy to its name. The Stanford Center for Narcolepsy was the first to report that narcolepsy-cataplexy is caused by hypocretin (orexin) abnormalities in both animal models and humans. Under the direction of Drs. Emmanuel Mignot and Seiji Nishino, the Stanford Center for Narcolepsy today treats several hundred patients with the disorder each year, many of whom participate in various research protocols. Other research protocols are conducted in animal models of narcolespy. We are always looking for volunteers in our narcolepsy research studies. We are presently recruiting narcoleptic patients for genetic studies, drug clinical trials, hypocretin measurement studies in the CSF and functional MRI studies. Monetary gifts to the Center for Narcolepsy are welcome. If you wish to make the ultimate gift, please consider participating in our Brain Donation Program. To advance our understanding of the cause, course, and treatment of narcolepsy, in 2001 Stanford University started a program to obtain human brain tissue for use in narcolepsy research. Donated brains provide an invaluable resource and we have already used previously donated brains to demonstrate that narcolepsy is caused by a lack of a very specific type of cell in the brain, the hypocretin (orexin) neuron. While the brain donations do not directly help the donor, they provide an invaluable resource and a gift to others. The real answers as to what causes or occurrs in the brain when one has narcolepsy will only be definitively understood through the study of brain tissue. Through these precious donations, narcolepsy may eventually be prevented or reversible. We currently are seeking brains from people with narcolepsy (with cataplexy and without), idiopathic hypersomnia and controls or people without a diagnosed sleep disorder of excessive sleepiness. Control brains are quite important to research, as findings must always be compared to tissue of a non-affected person. Friends and loved ones of people who suffer with narcoleps may wish to donate to our program to help fill this very important need. Refer to the Movies tab for movies of Narcolepsy / Cataplexy.brain tissue, brain, tissue, hypocretin, orexin, narcolepsy, sleep disorder, cataplexy, idiopathic hypersomnia, normal control, kleine-levin syndrome, dog, zebrafish, research, therapySCR_007021(Stanford Center for Narcolepsy, RRID:SCR_007021)Stanford University School of Medicine; California; USA Narcolepsy, Sleep disorder, Cataplexy, Idiopathic hypersomnia, Normal control, Kleine-Levin SyndromeIndividual gifts, NIHlisted by: One Mind Biospecimen Bank ListingLast checked downnlx_144254http://med.stanford.edu/school/Psychiatry/narcolepsy/
Spanish National Tumour Bank NetworkResource, topical portal, database, biomaterial supply resource, tissue bank, portal, material resource, data or information resourceTHIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. The need to use human neoplastic tissue under ideal conditions is currently of particular importance due to the development molecular pathology techniques that allow large-scale studies of genetic expression that are also of clinical significance. The Tumour Bank Network (TBN), instigated and coordinated by the Molecular Pathology Programme (MMP) aims to respond to this need by the promoting of Tumour Banks in Spanish hospitals. This will be achieved through the application of homogeneous procedures for the collection, processing and storage of neoplastic and normal tissue samples in such a way as to make molecular studies possible, avoiding that avoid the intrinsic bias of multi-centre studies possible. These Hospital Tumour Banks are based within the Pathology Departments of the collaborating Hospitals, that are interconnected through a computer-based network. In this way, each Centre''s tissue remains in the Hospital itself, thereby playing a key role in the development of the welfare, teaching and research activities within the Hospital. At the same time, it represents a tool to encourage of multi-hospital cancer research and of cooperation between basic and clinical researchers, constituting important collaboration between biomedical disciplines. The design does not correspond to a Central Tumour Bank, but that of a cooperative and coordinated Network of Hospital Banks, based on simple, homogeneous and optimal tissue treatment protocols. This Network is promoted by the Centro Nacional de Investigaciones Oncologicas (CNIO), which thereby undertakes the work of coordinating the network, using and maintaining the database, adhering to quality control. The aim of the CNIO's TBN is to acquire neoplastic and control non-neoplastic material of all types of malignant neoplasias, in the form of tissue fixed in formalin and paraffin embedded, of samples that are unfixed or frozen according to conventional methods as set out in Annexe 1 and even, exceptionally as fresh tissue. When other types of samples are required to carry out a specific project, the central office of the TBN will draw up a protocol with the group leading the project for the collection and maintenance of the tissue and clinicopathological data required for the proposed research. These protocols will be disseminated among the Associated Hospitals in order to gather the previously agreed number cases. Basic data surrounding the processing and preservation conditions for each case will be sent to the central office of the Bank, which under no circumstances will reveal the identity of the patient. Any Spanish cancer research team will be able to request tissue from the Tissue Bank Network. Absolute priority will be afforded to projects whose principal researcher belongs to one of the Associated Centres of the TNB, to other institutions with special agreements concerning the exchange of samples, and to the CNIO's researchers.clinical, neoplastic tissue, non-neoplastic tissue, tissue, fixed, formalin, paraffin embedded, unfixed, frozen, tumor, cancer, normal controlSCR_008707(Spanish National Tumour Bank Network, RRID:SCR_008707)Spanish National Cancer Research Center Tumor, Cancer, Normal controllisted by: One Mind Biospecimen Bank ListingLast checked downnlx_10273http://www.cnio.es/ing/programas/progTumor01.asp
Institute for Basic Research in Developmental DisabilitiesResource, topical portal, biomaterial supply resource, people resource, patient registry, tissue bank, brain bank, portal, graduate program resource, material resource, data or information resourceA research arm of the New York State Office for People with Developmental Disabilities (OPWDD), which conducts basic and clinical research into the causes, treatment, and prevention of intellectual disabilities and other developmental disabilities. The goals of the IBR's research, services and education program are designed to provide prevention, earlier detection, and improved treatment of intellectual disabilities and other developmental disabilities. This research program has a total of 46 laboratories over 7 departments. These programs include the George A. Jervis Clinic (a tertiary-level diagnostic and research clinic), the Specialty Clinical Laboratories (conduct specialty testing for genetic, metabolic, neurodegenerative disorders), and the Comprehensive Genetic Disease Program at Richmond County (provides genetics and genetic counseling services). This institute provides educational activities in the graduate studies program, and the Programs in Developmental Neuroscience and Developmental Disabilities (PDNDD). The PDNDD collaborates with the faculty from the City University of New York and the State University of New York. The IBR staff regularly conducts public education workshops and professional seminars about developmental disabilities.brain tissue, brain, tissue, developmental disability, late adult human, alzheimer's disease, autism, fragile x syndrome, taurine, fetal alcohol syndrome, batten disease, phenylketonuria, fetal development, down's syndrome, infant, development, biochemistry, neurobiology, genetics, molecular biology, neurochemistry, psychology, neuroscienceSCR_008806(Institute for Basic Research in Developmental Disabilities, RRID:SCR_008806)NYS Office for People With Developmental Disabilities Developmental disability, Aginglisted by: One Mind Biospecimen Bank ListingLast checked downnlx_144385http://www.opwdd.ny.gov/ws/ws_ibr_resources.jsp
Kidney Precision Medicine ProjectResource, disease-related portal, topical portal, organization portal, the community can contribute to this resource, consortium, nif annotation standard, narrative resource, portal, standard specification, project portal, availability annotation standard, data or information resourceProject to ethically obtain and evaluate human kidney biopsies from participants with Acute Kidney Injury (AKI) or Chronic Kidney Disease (CKD), create a kidney tissue atlas, define disease subgroups, and identify critical cells, pathways, and targets for novel therapies. Used to develop the next generation of software tools to visualize and understand the various components of kidney diseases and to optimize data collection. Multi site collaboration comprised of patients, clinicians, and investigators from across the United States.ethically, obtain, evaluate, human, kidney, biopsy, collaboration, patient, clinician, researcher, acute, injury, chronic, disease, tissue, atlas, cell, pathway, target, novel, therapy, data, collectionSCR_016920(Kidney Precision Medicine Project, RRID:SCR_016920)Acute Kidney Injury, Chronic Kidney DiseaseNIDDKlisted by: NIDDK Information Network, submitted by: NIDDK Information NetworkLast checked down
CREATEResource, topical portal, database, international standard specification, standard specification, narrative resource, portal, data or information resourceThe CREATE consortium represents a core of major European and international mouse database holders and research groups involved in conditional mutagenesis, primarily to develop a strategy for the integration and dissemination of Cre driver strains for modelling aspects of complex human diseases in the mouse. Collectively the participants have amassed a significant number of these strains in their respective databases. Therefore one of the goals of CREATE is to provide a unified portal for worldwide access to these critical resources. The portal can either be searched through an advanced BioMart interface, by driver name, or by anatomical site of expression using Embryonic Mouse Anatomy Project (EMAP) and Mouse Anatomy (MA) ontology terms. Search results link back to the original source of the data for more detailed information and to IMSR to order mice if available. The ontology browser is particularly useful as it enables the CREATE consortium to identify cell and tissues that are not currently covered by existing lines. CREATE also aims to coordinate the production of suitable lines by the Cre generation projects described above. Through the CREATE portal, the CREATE consortium aims to develop a strategy for the production, integration and dissemination of new Cre driver strains for modelling aspects of complex human diseases in the mouse. CREATE is also developing a roadmap for harnessing emerging technologies and methods for improving Cre-mediated recombination in vivo through targeted, intensive workshops and discussion forums on the portal. This will entail review of construct design options for classical transgenic constructs (promoter/enhancer used, small size <2025 Kb) vs large transgenic constructs (BAC, P1, YAC etc.); methods used for Cre transgenic lines including random vs targeted integration, position independent expression loci, or replacement of endogenous coding sequences with Cre recombinase under the control of the endogenous locus. CREATE provides a platform for discussion of additional issues specific to inducible Cre strategies including background activity before induction, inducibility (kinetics), efficiency, and protocols used for induction of Cre recombinase activity. Additional components of the technology roadmap will be the cataloguing of other existing methodologies (rtTA, FLP, Dre) of mouse genome modification, sharing information on validated Cre mutant lines as well as identification and assessment of new methods of mutagenesis such as RNAi and other emerging technologies. Other discussion topics addressed through surveys on the CREATE portal include the characterization of Cre lines (specificity of expression/deletion; efficiency of expression/ deletion; reproducibility of deletion from animal to animal for the same floxed allele; reproducibility with different floxed alleles; timing of expression/deletion, etc.), the extent to which Cre expression changes upon backcrossing to specific genetic backgrounds through variegation and silencing; potential phenotypes caused by either integration- mediated mutagenesis or Cre ''toxicity''; and other factors affecting the specificity of Cre-mediated expression/deletion. CREATE regularly integrates common fields from the Cre-X, CreZOO and the MGI recombinase portal resources described below. The data in common consists of: * Transgene or Knock-in name. * MGI ID of allele. * Driver. * Anatomical site of expression. * Pubmed ID. * IMSR strain name and link. * Inducibility (YES/NO).cre driver, mutagenesis, cre, gene, allele, mutant mouse es cell line, mutant mouse, es cell line, phenotype, gene expression, cre recombinase, tissue, organ, cell, mouse mutagenesis, cre lineSCR_006133(CREATE, RRID:SCR_006133)European Bioinformatics Institute European Union FP7related to: Recombinase (cre) ActivityPMID:21195764Last checked upnlx_151617
MTOPS Prostate Samples Analysis Consortium Resource, disease-related portal, topical portal, resource, research forum portal, portal, data or information resourceCross-disciplinary, multi-institutional network with a wide range of experts to analyze serum and tissue samples collected in the Medical Therapy of Prostatic Symptoms (MTOPS) trial. The consortium aims to discover and validate biomarkers for the detection, risk assessment, and disease progression assessment of benign prostatic hyperplasia (BPH). Analysis of the samples will also allow a biological evaluation of patients' responses to pharmacological treatments employed in MTOPS and correlation with BPH clinical parameters. Investigators will perform cooperative studies using the MTOPS material to evaluate genetic, immunologic, or biochemical biomarkers relevant to the progression of BPH, response-to-therapy, and the concurrent development of prostate cancer. The consortium will generate and validate biomarkers that will be made available to research community for use in a variety of investigations, including testing strategies for early detection, prevention, therapeutics, or imaging. The consortium will also produce research tools such as serum protein arrays, layered expression arrays, or tissue arrays that can be used by the research community. To identify novel targets for use as validated BPH markers, the consortium is currently exploring novel aspects of BPH biology and response to therapy. Several groups are using proteomic approaches, including SELDI, other types of mass spectrometry analysis, and 2D electrophoresis. Other groups are pursuing gene expression microarray analysis. The consortium is also organizing available data to identify current gaps. Groups with additional microarray data that has focused on BPH have compiled a common database of genes with expression patterns that are altered with the disease. This combined dataset will be used to identify some novel biomarkers revealed by single-site analyses. These novel biomarkers will then be validated using the tissues and serum microarrays that are being assembled. Another collaborative effort of the consortium involves construction of common tissue and serum resources and tissue microarrays (TMAs). Lists of available resources at each of the consortium member sites have been assembled along with information addressing secondary outcomes such as prediction of prostate growth and prediction of disease progression. Initial tissue microarrays composed of tissues from a number of sites have been constructed. Additional TMAs and serum microarrays are being constructed; these microarrays will be used by consortium members to aid in the validation of potential biomarkers. Participating in the MPSA network are one pathology-coordination center, six biomarker units, and a data coordinating center. The consortium comprises UT Southwestern, Vanderbilt University, Brigham and Women's Hospital, Harvard/University of Michigan, Baylor College of Medicine, University of Pittsburgh, and University of Colorado.prostate, male, adult human, biomarker, serum, tissue, microarraySCR_000041( MTOPS Prostate Samples Analysis Consortium , RRID:SCR_000041)NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases Benign Prostatic HyperplasiaNIDDKrelated to: NIDDK Information Network, affiliated with: Medical Therapy of Prostatic Symptoms, submitted by: NIDDK Information NetworkLast checked upnlx_152864
UCL BiobankResource, biomaterial supply resource, topical portal, portal, material resource, data or information resourceTwo University College London (UCL) biobanks, one based at the Royal Free Hospital (RFH) Campus and the other based at Bloomsbury supporting Pathology and the Cancer Institute, will act as physical repositories for collections of biological samples and data from patients consented at UCLH, Partners Hospitals and external sources. This will incorporate collections of existing stored samples and new collections. UCL-RFH BioBank, the physical repository at the Royal Free, presents a unique opportunity to advance medical research through making access to research tissue easier, faster and much more efficient. The BioBank is both a physical repository, with capacity for up to 1 million cryogenically stored samples and a virtual repository for all tissue, cell, plasma, serum, DNA and RNA samples stored throughout UCLP. In particular, samples considered "relevant material", such as tissues and cells, that are licensed by the Human Tissue Authority, can be stored long term. Existing holdings of tissues and cells where appropriate can be transferred to the Physical BioBank at the Royal Free. UCL - Royal Free BioBank provides a flexible approach to banking, allowing the Depositor to pick and choose services that are tailored to fit their requirements. Collaborations arising from publicizing of the existence of the holdings are entirely at the discretion of the depositor, as the facility ensures that access to the deposits remains at the decision of the Depositor/User. UCL Biobank for studying Health and Disease (based at Pathology-Rockefeller building and the UCL-Cancer Institute will support projects principally involved in the study of human disease. The aim is to support primarily, research in the Pathology Department, UCLH and the UCL-Cancer Institute but it will also support other UCLH partners. The biobank will store normal and pathological specimens, surplus to diagnostic requirements, from relevant tissues and bodily fluids. Stored tissues will include; snap-frozen or cryopreserved tissue, formalin-fixed tissue, paraffin-embedded tissues, and slides prepared for histological examination. Tissues will include resection specimens obtained surgically or by needle core biopsy. Bodily fluids will include; whole blood, serum, plasma, urine, cerebrospinal fluid, milk, saliva and buccal smears and cytological specimens such as sputum and cervical smears. Fine needle aspirates obtained from tissues and bodily cavities (e.g. pleura and peritoneum) will also be collected. Where appropriate the biobank will also store separated cells, protein, DNA and RNA isolated from collected tissues and bodily fluids described above. Some of the tissue and aspirated samples will be stored in the diagnostic archive.tissue, cell, plasma, serum, dna, rna, blood, serum, plasma, urine, cerebral spinal fluid, milk, saliva, buccal smear, sputum, cervical smear, pleura, peritoneum, protein, body fluid, cryopreserved, frozen, snap-frozen, formalin-fixed, paraffin-embedded, slide, cancer, disease, normalSCR_000517(UCL Biobank, RRID:SCR_000517)University College London; London; United Kingdom Cancer, Disease, Normallisted by: One Mind Biospecimen Bank ListingLast checked upnlx_36620
Autism Tissue ProgramResource, disease-related portal, topical portal, database, portal, funding resource, data or information resourceAutism research program that makes available post-mortem brain tissue to qualified scientists all over the world. Working directly with tissue banks, organ procurement agencies, medical examiners and the general public, this is the largest program dedicated to increasing and enhancing the availability of post-mortem brain tissue for basic research in autism. To date, the ATP has collected and stored more than 170 brains in their repositories at Harvard (US) and Oxford (UK). These brains are processed by formalin fixation and/or snap frozen to properly provide high quality tissue of all brain regions, in support of biological research in autism. The ATP is unique in that they diligently pursue all available clinical data (pre and post mortem) on tissue donors in order to create the most biologically relevant brain repository for autism research. These data, together with tissue resources from both banks and associated repositories, are presented to all interested researchers through their extensive web-based data portal (login required). The ATP is not a brain bank, but works directly with the Harvard Brain Tissue Resource Center in Boston (HBTRC), Massachusetts to serve as its tissue repository. This program augments brain bank functions by: * Creating the most biologically relevant brain tissue repository possible * Fully covering all costs associated with brain extraction and transfer to the repositories at Harvard (US and Canada) and Oxford (UK). * Providing scientific oversight of tissue distributions * Overseeing and managing all tissue grants * Clinically phenotyping and acquiring extensive medical data on all of their donors * Providing continuing family support and communication to all of their donors * Directly supporting researchers to facilitate autism research * Maintaining a robust web based data management and secure on-line global interface system * Developing and supporting ATP established scientific initiatives * Actively providing public outreach and education The ATP is not a clinical organ procurement agency, but rather they facilitate the wishes of donors and families to donate their tissue to autism research. Through the ATP's established international infrastructure, they work with any accredited tissue bank, organ procurement agency, or medical examiner that receives a family's request to donate their loved one's tissue to the program. Once contacted, the ATP will insure that the family's request to donate their loved one's tissue is faithfully met, covering all costs to the family and partnering agency as well as ensuring the tissues' proper and rapid transport to the ATP's repository at the Harvard Brain Tissue Resource Center (HBTRC) in Boston, Massachusetts.autism, brain, tissue, clinical data, post-mortem, brain tissue, donate, brain donation, autism spectrum disorder, pervasive development disorder, formalin fixation, snap frozen, tissue section, stained slide, dna, skin fibroblast culture, control, clinical, clinical neuroinformatics, imaging genomics, magnetic resonance, optical imagingSCR_000651(Autism Tissue Program, RRID:SCR_000651) Harvard Brain Tissue Resource Center , Autism Speaks Autism, Autism spectrum disorder, Pervasive Development Disorder, ControlAutism Speakslisted by: NeuroImaging Tools and Resources Collaboratory (NITRC)Last checked upnif-0000-10160http://www.nitrc.org/projects/atp, http://www.brainbank.org/, http://www.autismtissueprogram.org/site/c.nlKUL7MQIsG/b.5183271/k.BD86/Home.htm
DIAN - Dominantly Inherited Alzheimer NetworkResource, disease-related portal, topical portal, database, biomaterial supply resource, tissue bank, portal, brain bank, material resource, data or information resourceAn international research partnership of leading scientists determined to understand a rare form of Alzheimers disease that is caused by a gene mutation and to establish a research database and tissue repository to support research on Alzheimers disease by other investigators around the world. One goal of DIAN is to study possible brain changes that occur before Alzheimers disease is expressed in people who carry an Alzheimers disease mutation. Other family members without a mutation will serve as a comparison group. People in families in which a mutation has been identified will be tracked in order to detect physical or mental changes that might distinguish people who inherited the mutation from those who did not. DIAN currently involves eleven outstanding research institutions in the United States, United Kingdom, and Australia. John C. Morris, M.D., Friedman Distinguished Professor of Neurology at Washington University School of Medicine in St. Louis, is the principal investigator of the project.gene mutation, dementia, cerebrum, image, middle frontal gyrus, superior temporal gyri, middle temporal gyri, inferior parietal lobe, angular gyrus, occipital lobe, calcarine sulcus, peristriate cortex, anterior cingulate gyrus, genu of the corpus callosum, posterior cingulate gyrus, precuneus, splenium, amygdala, entorhinal cortex, hippocampus, parahippocampal gyrus, striatum, caudate nucleus, anterior commissure, lentiform nuclei, globus pallidus, putamen, thalamus, subthalamic nucleus, midbrain, pons, medulla oblongata, cerebellum, dentate nucleus, spinal cord, frontal lobe, temporal lobe, mamillary body, parietal lobe, lateral geniculate nucleus, occipital lobe, calcarine sulcus, cerebellar hemisphere, dentate nucleus, clinical dementia rating, geriatric depression scale, functional assessment questionnaire, neuropsychiatric inventory-q, united parkinsons disease rating scale (updrs)-motor, hachinski ischemic score, cerebrovascular risk factor, cerebral spinal fluid, plasma, serum, blood, brain tissue, brain, tissue, formalin-fixed, paraffin wax embedded, block, frozen, clinical data, clinical, demographics, psychometrics, apoe genotype, adult human, mri, positron emission tomography, clinical assessment, psychometric testingSCR_000812(DIAN - Dominantly Inherited Alzheimer Network, RRID:SCR_000812)Washington University School of Medicine in St. Louis; Missouri; USA Dominantly inherited Alzheimer's disease, Biological adult child of a parent with a mutated gene known to cause dominantly inherited Alzheimer's disease, Alzheimer's disease, Normal control, AgingNIArelated to: National Cell Repository for Alzheimer's Disease, listed by: One Mind Biospecimen Bank Listing, NeuroImaging Tools and Resources Collaboratory (NITRC)Last checked upnlx_149316
Pediatric Acute Liver Failure Study Resource, disease-related portal, topical portal, resource, research forum portal, portal, data or information resourceStudy group and network for a 2008 longitudinal study for the etiology, diagnosis, treatment, and outcome of acute liver failure in infants, children, and adolescents. Data from patients include urine, bile, serum, liver tissue, cell lines derived from fibroblast culture, and DNA.management strategy, infant, child, adolescent, clinical, liver, patient care, rare disease, blood, tissue, longitudinal, urine, bile, serum, liver tissue, cell line, fibroblast culture, dna, etiology, diagnosis, treatment, outcomeSCR_001478( Pediatric Acute Liver Failure Study , RRID:SCR_001478)University of Pittsburgh; Pennsylvania; USA Acute liver failureNIDDKrelated to: Acute Liver Failure Study Group, listed by: NIDDK Information Network, submitted by: NIDDK Information NetworkLast checked upnlx_152715http://www.palfstudy.org/documents/PALFAncillaryStudyPolicyv2.5.pdf
Ataxia-Telangiectasia Childrens ProjectResource, disease-related portal, topical portal, portal, data or information resourceThe Ataxia Telangiectasia Children's Project, better known as the A-T Children's Project, was founded in late 1993 by a family in Florida with two young sons who have A-T. It is a public, tax-exempt, non-profit organization pursuant to Section 501(c)(3) of the Internal Revenue Code, and all gifts and donations to the Project are tax deductible. The A-T Children's Project was formed to raise funds through events and contributions from corporations, foundations and friends. These funds are then used to accelerate first-rate, international scientific research aimed at finding a cure and improving the lives of all children with ataxia-telangiectasia. - To encourage and support excellent laboratory research which will accelerate the discovery of a cure or possible therapies for ataxia-telangiectasia by: - awarding competitive research grants to top scientists using a peer-review board comprised of top scientists and physicians, - organizing and sponsoring workshops and symposiums in order to encourage cooperation among laboratories and to generate new research strategies, and - working with Congress and the National Institutes of Health to encourage the funding of active research on A-T by agencies of the U.S. government. - To improve the accurate and timely diagnosis of A-T patients by increasing public awareness and by educating physicians. - To develop and maintain an international patient registry of A-T patients with objective, neutral oversight, while leaving ultimate control in the hands of treating physicians, so that up-to-date clinical information about A-T patients can be obtained for researchers and so that when a treatment is developed, all patients can be reached through their physicians. - To support and oversee a clinical center and information clearinghouse at a top-rated, world-class medical center for the evaluation of A-T patients by a multidisciplinary team of specialists, and for the accumulation of experience in managing the many facets of A-T such as the ataxia, cancer and immune problems. - To develop quantitative endpoints for objectively measuring the progression rate and severity of the symptoms of A-T. - To maintain and enlarge a tissue/cell bank with objective, neutral oversight and control in order to ensure free access of existing and new researchers to A-T patient specimens. Sponsors: The A-T Children's Project is a non-profit organization that raises funds to support and coordinate first-rate biomedical research projects, scientific conferences and a clinical center aimed at finding a cure or life-improving therapies for ataxia-telangiectasia, a lethal genetic disease that attacks children, causing progressive loss of muscle control, immune system problems, and a strikingly high rate of cancer, especially leukemia and lymphoma.education, funding, ataxia, ataxia telangiectasia, cancer, cell, cure, immune, international, laboratory, physician, research, scientific, scientist, telangiectasia, tissue, tissue bankSCR_001671(Ataxia-Telangiectasia Childrens Project, RRID:SCR_001671)Last checked upnif-0000-10158
Internet Atlas of HistologyResource, topical portal, curriculum material, narrative resource, slide, training material, portal, data or information resourceThis portal leads to the Internet Atlas of Histology. This atlas allows you to explore the complete set of histological specimens that features many excellent plastic sections prepared by Aulikki Kokko-Cunningham, M.D. Also called University of Illnois at Urbana-Champaign, the College of Medicine: Internet Atlas of Histology Over 1000 labeled histological features are labeled and have accompanying functional descriptions. All of this information is accessible though an alphabetical index and a search engine. This resource has images categorized in: - Slides: Links to all of the specimens - Objects:Index of histological features Sponsors: This resource is supported by UIUC.electron micrograph, electron microscopy, endocrine, epithelium, female reproductive system, blood, bone, bone marrow, cell, circulatory system, connective tissue, cross section, digestive tract, histology, immune system, light microscopy, male reproductive system, muscle, nervous system, object, respiratory system, scanning electron microscopy (sem), sense organ, skin, specimen, tissue, transmission electron microscopy (tem), urinary system, imageSCR_001745(Internet Atlas of Histology, RRID:SCR_001745)University of Illinois at Urbana-Champaign; Illinois; USA Last checked upnif-0000-10251
International Union of Physiological Sciences: Physiome ProjectResource, topical portal, portal, data or information resourceThe Physiome Project is a worldwide public domain effort to provide a computational framework for understanding human and other eukaryotic physiology. It aims to develop integrative models at all levels of biological organization, from genes to the whole organism via gene regulatory networks, protein pathways, integrative cell function, and tissue and whole organ structure/function relations. Additionally, an important goal of the project is to develop applications for teaching physiology. Current projects include the development of: - ontologies to organize biological knowledge and access to databases - markup languages to encode models of biological structure and function in a standard format for sharing between different application programs and for re-use as components of more comprehensive models - databases of structure at the cell, tissue and organ levels - software to render computational models of cell function such as ion channel electrophysiology, cell signaling and metabolic pathways, transport, motility, the cell cycle, etc. in 2 & 3D graphical form - software for displaying and interacting with the organ models which will allow the user to move across all spatial scales Sponsors: This project is supported by the International Union of Physiological Sciences (IUPS), the IEEE Engineering. in Medicine and Biology (EMBS), and the International Federation for Medical and Biological Engineering (IFMBE)electrophysiology, eukaryotic, framework, function, gene, 3d form, biological, cell, cell cycle, channel, computational, human, ion, metabolic, model, motility, network, organ, organism, pathway, physiology, physiome, protein, public domain, regulatory, signaling, software, structure, tissue, transportSCR_001760(International Union of Physiological Sciences: Physiome Project, RRID:SCR_001760)Last checked upnif-0000-10266
Center for Bio-Image InformaticsResource, topical portal, data or information resource, portal, databaseThe Center for Bio-Image Informatics is an interdisciplinary research effort between Biology, Computer Science, Statistics, Multimedia and Engineering. The overarching goal of the center is the advancement of human knowledge of the complex biological processes which occur at both cellular and sub-cellular levels. the center employs and develops cutting edge techniques in the fields of imaging, pattern recognition and data mining. Research also focuses on development of new information processing techniques which can afford us a better understanding of biological processes depicted in microscopy images of cells and tissues, specifically on the distributions of biological molecules within these samples. This is achieved by borrowing methods for information processing at the sensor level to enable high speed and super-resolution imaging. By applying pattern recognition and data mining methods to bio-molecular images, full automation of both the extraction of information and the construction of statistically-sound models of the processes depicted in those images was possible. At the heart of the center's reseach is the BISQUE system, an online repository for multidimensional bio-images, and testbed for new research techniques and methods. BISQUE: Online Semantic Query User Environment is an online database for managing up to 5 dimensional scientific images with associated metadata and a flexible, collaborative tagging system. Currently the system has more than 85,000 user-provided tags and 128006 2-D planes from over 6,000 biological images. BISQUE is much more than just a repository for scientific images- the system provides resources for complex scientific analysis over images, result visualization, user-extensible modules, customized organization of images, advanced search features, graphical annotations, textual annotations and compatible client-side applications. Sponsors: This work is supported in part by an NSF infrastructure award No. EIA-0080134 and IIS-0808772.engineering, biological image, biological molecule, biological process, biology, cell, cellular, computer science, graphical annotation, metadata, microscopy, multimedia, semantic, statistics, sub-cellular, tagging system, textual annotation, tissueSCR_001949(Center for Bio-Image Informatics, RRID:SCR_001949)University of California at Santa Barbara; California; USA Last checked upnif-0000-10523
Cancer Genome Anatomy ProjectResource, topical portal, portal, data or information resourceProject to determine the gene expression profiles of normal, precancer, and cancer cells, whose generated resources are available to the cancer community. Interconnected modules provide access to all CGAP data, bioinformatic analysis tools, and biological resources allowing the user to find in silico answers to biological questions in a fraction of the time it once took in the laboratory. * Genes * Tissues * Pathways * RNAi * Chromosomes * SAGE Genie * Toolsgene, gene expression, normal cell, precancer cell, cancer cell, cell, genome, anatomy, gene expression profile, tissue, pathway, rnai, chromosomeSCR_003072(Cancer Genome Anatomy Project, RRID:SCR_003072)National Cancer Institute Cancer, Normal, PrecancerNCILast checked upnif-0000-30468
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