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http://www.progeriaresearch.org/cell_tissue_bank.html

The PRF Cell & Tissue Bank provides medical researchers with genetic and biological material from Progeria patients and their families, so that research on Progeria and other age-related diseases can be performed. We''ve been hard at work with the families and their physicians to gather these precious biological materials. As you know, Hutchinson-Gilford Progeria Syndrome is an extremely rare condition. Thus while access to cell lines is essential for studying the biology and genetics of the disorder, there are very few cell lines in existence. Because an integral part of PRF''s mission is to stimulate interest in, and NIH funding opportunities for, Progeria research, there is an increased need for cell lines. The PRF Cell Bank will ensure that need is met! The goals of The PRF Cell & Tissue Bank are to promote: * Sufficient availability of cells for approved research projects * Incentive for new research projects * Study of the biochemical basis for Hutchinson-Gilford Progeria Syndrome * Discoveries leading to new treatments for children with Progeria * Discovery of a cure for Progeria

Proper citation: Progeria Cell and Tissue Bank (RRID:SCR_004194) Copy   

•   Source: SciCrunch Registry

http://www.genewiz.com

Commercial organization for research and development genomics services and technical support to researchers.

Proper citation: GENEWIZ (RRID:SCR_003177) Copy   

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http://www.t-profiler.org

One of the key challenges in the analysis of gene expression data is how to relate the expression level of individual genes to the underlying transcriptional programs and cellular state. The T-profiler tool hosted on this website uses the t-test to score changes in the average activity of pre-defined groups of genes. The gene groups are defined based on Gene Ontology categorization, ChIP-chip experiments, upstream matches to a consensus transcription factor binding motif, and location on the same chromosome, respectively. If desired, an iterative procedure can be used to select a single, optimal representative from sets of overlapping gene groups. A jack-knife procedure is used to make calculations more robust against outliers. T-profiler makes it possible to interpret microarray data in a way that is both intuitive and statistically rigorous, without the need to combine experiments or choose parameters. Currently, gene expression data from Saccharomyces cerevisiae and Candida albicans are supported. Users can submit their microarray data for analysis by clicking on one of the two organism-specific tabs above. Platform: Online tool

Proper citation: T-profiler (RRID:SCR_003452) Copy   

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http://www.gensat.org/retina.jsp

Collection of images from cell type-specific protein expression in retina using BAC transgenic mice. Images from cell type-specific protein expression in retina using BAC transgenic mice from GENSAT project.

Proper citation: Retina Project (RRID:SCR_002884) Copy   

•   Source: SciCrunch Registry

http://dire.dcode.org

Web server based on the Enhancer Identification (EI) method, to determine the chromosomal location and functional characteristics of distant regulatory elements (REs) in higher eukaryotic genomes. The server uses gene co-expression data, comparative genomics, and combinatorics of transcription factor binding sites (TFBSs) to find TFBS-association signatures that can be used for discriminating specific regulatory functions. DiRE's unique feature is the detection of REs outside of proximal promoter regions, as it takes advantage of the full gene locus to conduct the search. DiRE can predict common REs for any set of input genes for which the user has prior knowledge of co-expression, co-function, or other biologically meaningful grouping. The server predicts function-specific REs consisting of clusters of specifically-associated TFBSs, and it also scores the association of individual TFs with the biological function shared by the group of input genes. Its integration with the Array2BIO server allows users to start their analysis with raw microarray expression data.

Proper citation: Distant Regulatory Elements (RRID:SCR_003058) Copy   

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http://www.genscript.com/psort/wolf_psort.html

Data analysis service for protein subcellular localization prediction.

Proper citation: WoLF PSORT (RRID:SCR_002472) Copy   

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http://www.lerner.ccf.org/gmi/gmb/

A biorepository is a place where investigators can deposit and store biological material, in this case samples derived from patients. Moreover, the Genomic Medicine Institute (GMI) takes this basic concept and elevates it to make the Genomic Medicine Biorepository (GMB) a full-service processing and banking laboratory that serves as the foundation for evidence-based research for the GMI, the Cleveland Clinic, and our collaborators. The process relies on a team of multi-disciplinary professionals coordinating their efforts in order to streamline medical research. This begins with dedicated physicians and genetic counselors identifying individuals with specific medical conditions indicating the possibility of genetic involvement. Once identified, biological material (e.g. blood, tissue, or saliva) is collected under the care of the patient''s doctor or by our clinicians and sent to the GMB. Once in the lab, the patient and their samples are assigned a unique identifier (to protect the patient''s personal information) and logged into a central database. This unique identifier accompanies all samples processed and banked for that individual. The specimens are then processed into research-relevant samples using proven laboratory techniques and state-of-the-art quality control practices. These samples include the isolation of DNA and RNA from white blood cells for genetic studies; collection of plasma for proteomic studies; and initiated immortalized cell lines from lymphocytes for in-vitro studies and biochemical research. These cell lines are able to be indefinitely stored in cryogenic suspension and are invaluable as a renewable resource for genetic and biochemical research. The GMB also processes genetic material from various tissues (both fresh and archived). Charis Eng, MD, PhD, Chair and Director of the GMI, has been the faculty oversight person of a human biorepository for the last eight years. Since then, our biorepository has received, cataloged, processed, and banked, in excess of 25,000 specimens. These samples are of numerous tissue types from patients and their family members located all over the world. Our biorepository has managed samples that have resulted in more than 150 original peer reviewed articles and greater than $25 million total direct costs in extramural funding over the last four years alone.

Proper citation: Cleveland Clinic Genomic Medicine Biorepository (RRID:SCR_004136) Copy   

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http://sadiframework.org/

Framework for discovery of, and interoperability between, distributed data and analytical resources. It combines GET/POST-based Web Services with standards from the W3C Semantic Web initiative. The objective is to make it easy for data and analytical tool providers to make their resources available on the Semantic Web with minimal disruption to their usual practices. It simply defines an open set of best-practices and conventions, within the spectrum of existing standards, that allow for a high degree of semantic discoverability and interoperability between participating services.

Proper citation: Semantic Automated Discovery and Integration (RRID:SCR_004130) Copy   

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http://www.mouseconnectome.org/

Three-dimensional digital connectome atlas of the C57Black/6J mouse brain and catalog of neural tracer injection cases, which will eventually cover the entire brain. Serial sections of each case are available to view at 10x magnification in the interactive iConnectome viewer. The Image Gallery provides a glimpse into some of the highlights of their data set. Representative images of multi-fluorescent tracer labeling can be viewed, while more in depth examination of these and all other cases can be performed in the iConnectome viewer. Phase 1 of this project involves generating a physical map of the basic global wiring diagram by applying proven, state of the art experimental circuit tracing methods systematically, uniformly, and comprehensively to the structural organization of all major neuronal pathways in the mouse brain. Connectivity imaging data for the whole mouse brain at cellular resolution will be presented within a standard 3D anatomic frame available through the website and accompanied by a comprehensive searchable online database. A Phase 2 goal for the future will allow users to view, search, and generate driving direction-like roadmaps of neuronal pathways linking any and all structures in the nervous system. This could be looked on as a pilot project for more ambitious projects in species with larger brains, such as human, and for providing a reliable framework for more detailed local circuitry mapping projects in the mouse.

Proper citation: Mouse Connectome Project (RRID:SCR_004096) Copy   

•   Source: SciCrunch Registry

http://www.escholarship.org/

Provides comprehensive publication services for Univeristy of California affiliated departments, research units, publishing programs, and individual scholars who seek to publish original, open access journals, books, conference proceedings, and other scholarship. Content is delivered via research platform and is available to scholars worldwide.

Proper citation: eScholarship (RRID:SCR_002624) Copy   

•   Source: SciCrunch Registry

http://hgc.rockefeller.edu/

An interactive web server that enables researchers to prioritize any list of genes by their biological proximity to defined core genes (i.e. genes that are known to be associated with the phenotype), and to predict novel gene pathways.

Proper citation: Human Gene Connectome Server (RRID:SCR_002627) Copy   

•   Source: SciCrunch Registry

http://www.core.org/

The Center for Organ Recovery & Education (CORE) is one of 58 federally designated agencies in the United States known as a not-for-profit organ procurement organization (OPO). CORE is dedicated to promoting donation, education and research for the purpose of saving and improving the quality of life through organ, tissue and corneal transplantation. An innovative, responsive OPO, CORE plays a pivotal role between potential donors and patients awaiting transplantation. In addition to talking with families about the opportunity to donate, CORE coordinates the surgical recovery of organs, tissue and corneas, as well as the computerized matching of donated organs and placement of corneas. In 1995, CORE created the first donor card database in Pennsylvania. In 1996, the organization added tissue recovery and eye banking services to its organ recovery component. It enhanced its line of services by opening an internal laboratory in 1997, where CORE performs the necessary tests to help determine if the organs, tissue and corneas are healthy for transplantation. Since its inception more than 30 years ago, CORE has helped to provide more than 300,000 organs, tissue and corneas for transplantation. The chances for renewed health provided through CORE would not be possible without those who have said yes to donation.

Proper citation: Center for Organ Recovery and Education - CORE (RRID:SCR_004317) Copy   

•   Source: SciCrunch Registry

https://komentissuebank.iu.edu/

The goals of the Susan G. Komen for the Cure Tissue Bank at the IU Simon Cancer Center are to acquire biomolecule and tissue specimens from the entire continuum of breast development: puberty to menopause and to make these specimens or the digital data derived from them available and accessible to researchers across the globe.

Proper citation: Susan G. Komen Tissue Bank (RRID:SCR_004708) Copy   

•   Source: SciCrunch Registry

http://www.life-source.org/

LifeSource is the non-profit organization dedicated to saving lives through organ and tissue donation in the Upper Midwest. We serve more than 6 million people in communities across Minnesota, North Dakota, South Dakota and portions of western Wisconsin. As the federally-designated organization that manages organ and tissue donation in our region, we are dedicated to working with our hospital and community partners to support donor families, facilitate the donation of organs and tissues to transplant recipients and encourage the people in our communities to register as donors.

Proper citation: LifeSource (RRID:SCR_004702) Copy   

•   Source: SciCrunch Registry

http://tissuebank.stanford.edu/

The Stanford Tissue Bank was established with seed funding from the Bio-X Program and the Department of Pathology, and currently receives support from the Stanford Cancer Institute. The goal of the Tissue Bank is to facilitate biomedical research using tissues at Stanford, by providing services for the procurement, storage, distribution, and study of tissues. Current Tissue Bank activities and services include collecting and banking freshly-frozen tissue specimens from excess surgical material and from autopsy, providing fresh tissue specimens for viable cell studies, processing and banking blood components, maintaining a tissue database with links to clinicopathological data, performing histological staining and pathological review, and coordinating patient consent and assuring regulatory compliance. As a centralized shared resource, the Tissue Bank adds value through experience, efficiency, standardization, accountability, protection of patient confidentially, and timely completion of research. An oversight committee serves to guide policies, prioritize resources, and review service requests to ensure equitable usage.

Proper citation: Stanford Tissue Bank (RRID:SCR_004615) Copy   

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http://acsr.ucsf.edu/

A biorepository for HIV-infected human biospecimens from a wide spectrum of HIV-related or associated diseases, including cancer, and from appropriate HIV-negative controls. The ACSR has formalin-fixed paraffin embedded biospecimens, fresh frozen biospecimens, malignant cell suspensions, fine needle aspirates, and cell lines from patients with HIV-related malignancies. It also contains serum, plasma, urine, bone marrow, cervical and anal specimens, saliva, semen, and multi-site autopsy speicmens from patients with HIV-related malignancies including those who have participated in clinical trials. The ACSR has an associated databank that contains prognostic, staging, outcome and treatment data on patients from whom tissues were obtained. The ACSR database contains more than 300,000 individual biospecimens with associated clinical information. Biospecimens are entered into the ACSR database by processing type, disease category, and number of cases defined by disease category.

Proper citation: AIDS and Cancer Specimen Resource (RRID:SCR_004216) Copy   

•   Source: SciCrunch Registry

http://www.walescancerbank.com/

The Wales Cancer Bank aims to collect samples of tumour, normal tissue and blood from all patients in Wales who are undergoing an operation to remove tissue where cancer is a possible diagnosis. These samples will be banked to build up a research resource that will be used by research groups to help understand the molecular mechanisms involved in cancer and work towards the selection of optimum targeted treatment for individuals. The Wales Cancer Bank is licensed by the Human Tissue Authority (license 12107) to store human tissue for research and has ethics approval from the Wales Multicentre Research Ethics Committee to collect and issue samples for cancer related research.

Proper citation: Wales Cancer Bank (RRID:SCR_004331) Copy   

•   Source: SciCrunch Registry

https://scicrunch.org/browse/resourcesedit/SCR_004214

THIS RESOURCE IS NO LONGER IN SERVICE, documented May 18, 2022. A tumor bank that provides a large collection of cancer specimens, from breast and other cancers, annotated with clinical information. The CBCF TB enables researchers to address unanswered questions concerning the prognosis and treatment of breast cancer and other cancers. The CBCF TB website is also directed to participants interested in donating tumor tissue or blood. Biological specimens such as blood, urine, bone marrow, and ascites (fluid that sometimes collects in the abdomen) contain genetic information, just as tumor tissue does. These samples can be used in studies that may help researchers see how people with certain genetic make-ups respond to certain treatments. It can also explain why different people have different health problems. CBCF TB, formerly ARTB, was created by a merger of components of two existing Tumor-banking initiatives, the CLS Repository in Calgary and the Tumor bank of the PolyomX Program in Edmonton.

Proper citation: Canadian Breast Cancer Foundation Tumor Bank (RRID:SCR_004214) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/thornton-srv/databases/profunc/index.html

The ProFunc server had been developed to help identify the likely biochemical function of a protein from its three-dimensional structure. It uses both sequence- and structure-based methods including fold matching, residue conservation, surface cleft analysis, and functional 3D templates, to identify both the protein''''s likely active site and possible homologues in the PDB. Often, where one method fails to provide any functional insight another may be more helpful. You can submit your own structure, analyze an existing PDB entry, or retrieve the results of a previously submitted run. The files are usually stored for about 6 months before being deleted. However, they are stored on a partition that is not backed up; so, in principle, they could disappear at any time.

Proper citation: ProFunc (RRID:SCR_004450) Copy   

•   Source: SciCrunch Registry

http://www.gsds.org/Home%20Page

Golden State Donor Services (GSDS) is the nonprofit, federally designated transplant donor network serving two and a half million people in the greater Sacramento area. We are committed to saving and improving lives by connecting one life to another through donation and transplantation. We support potential donor families in their time of loss, provide care for them through the donation process and coordinate the recovery of organs and tissues for transplant. We also provide after-care support to donor families while at the same time working to inspire universal acceptance of donation to ensure every person in need receives the ����??Gift of Life.����?? GSDS'' designated service area includes 11 counties in Northern California, (Amador, Calaveras, Colusa, El Dorado, Nevada, Placer, Sacramento, Sierra, Sutter, Yolo, and Yuba), as well as the communities of Santa Rosa and Reno. Currently GSDS has agreements with 30 hospitals. In Golden State Donor Services'' area, more than 1000 people now wait for an organ transplant, (heart, liver, lungs, kidneys, intestine or pancreas).

Proper citation: GSDS - Golden State Donor Services (RRID:SCR_004605) Copy   

•   Source: SciCrunch Registry