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https://cghub.ucsc.edu/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 17, 2022. A secure repository for storing, cataloging, and accessing cancer genome sequences, alignments, and mutation information from the Cancer Genome Atlas (TCGA) consortium and related projects. CGHub gives scientific researchers the statistical power of large cancer genome datasets to attack the molecular complexity of cancer.

Proper citation: Cancer Genomics Hub (RRID:SCR_002657) Copy   

•   Source: SciCrunch Registry

http://www.dtp.nci.nih.gov

Portal for preclinical information and research materials, including web-accessible data and tools, NCI-60 Tumor Cell Line Screen, compounds in vials and plates, tumor cells, animals, and bulk drugs for investigational new drug (IND)-directed studies. DTP has been involved in the discovery or development of more than 70 percent of the anticancer therapeutics on the market today, and will continue helping the academic and private sectors to overcome various therapeutic development barriers, particularly through supporting high-risk projects and therapeutic development for rare cancers. Initially DTP made its drug discovery and development services and the results from the human tumor cell line assay publicly accessible to researchers worldwide. At first, the site offered in vitro human cell line data for a few thousand compounds and in vitro anti-HIV screening data for roughly 42,000 compounds. Today, visitors can find: * Downloadable in vitro human tumor cell line data for some 43,500 compounds and 15,000 natural product extracts * Results for 60,000 compounds evaluated in the yeast assay * In vivo animal model results for 30,000 compounds * 2-D and 3-D chemical structures for more than 200,000 compounds * Molecular target data, including characterizations for at least 1,200 targets, plus data from multiple cDNA microarray projects In addition to browsing DTP's databases and downloading data, researchers can request individual samples or sets of compounds on 96-well plates for research, or they can submit their own compounds for consideration for screening via DTP's online submission form. Once a compound is submitted for screening, researchers can follow its progress and retrieve data using a secure web interface. The NCI has collected information on almost half a million chemical structures in the past 50 years. DTP has made this information accessible and useful for investigators through its 3-D database, a collection of three-dimensional structures for more than 200,000 drugs. Investigators use the 3-D database to screen compounds for anticancer therapeutic activity. Also available on DTP's website are 127,000 connection tables for anticancer agents. A connection table is a convenient way of depicting molecular structures without relying on drawn chemical structures. As unique lists of atoms and their connections, the connection tables can be indexed and stored in computer databases where they can be used for patent searches, toxicology studies, and precursor searching, for example., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Developmental Therapeutics Program (RRID:SCR_003057) Copy   

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http://seer.cancer.gov/

SEER collects cancer incidence data from population-based cancer registries covering approximately 47.9 percent of the U.S. population. The SEER registries collect data on patient demographics, primary tumor site, tumor morphology, stage at diagnosis, and first course of treatment, and they follow up with patients for vital status.There are two data products available: SEER Research and SEER Research Plus. This was motivated because of concerns about the increasing risk of re-identifiability of individuals. The Research Plus databases require more rigorous process for access that includes user authentication through Institutional Account or multiple-step request process for Non-Institutional users.

Proper citation: Surveillance Epidemiology and End Results (RRID:SCR_006902) Copy   

•   Source: SciCrunch Registry

https://cansar.icr.ac.uk/

canSAR is an integrated database that brings together biological, chemical, pharmacological (and eventually clinical) data. Its goal is to integrate this data and make it accessible to cancer research scientists from multiple disciplines, in order to help with hypothesis generation in cancer research and support translational research. This cancer research and drug discovery resource was developed to utilize the growing publicly available biological annotation, chemical screening, RNA interference screening, expression, amplification and 3D structural data. Scientists can, in a single place, rapidly identify biological annotation of a target, its structural characterization, expression levels and protein interaction data, as well as suitable cell lines for experiments, potential tool compounds and similarity to known drug targets. canSAR has, from the outset, been completely use-case driven which has dramatically influenced the design of the back-end and the functionality provided through the interfaces. The Web interface provides flexible, multipoint entry into canSAR. This allows easy access to the multidisciplinary data within, including target and compound synopses, bioactivity views and expert tools for chemogenomic, expression and protein interaction network data.

Proper citation: canSAR (RRID:SCR_006794) Copy   

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http://www.ariad.com/

Cambridge, Massachusetts-based biotechnology company focused on cancer. Focus areas are blood cancers and solid tumors. Compounds: ponatinib, AP26113, ridaforolimus and AP1903., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: ARIAD (RRID:SCR_008559) Copy   

•   Source: SciCrunch Registry

http://www.zbh.uni-hamburg.de/?id=292

A web-based software tool for the integrative analysis of cancer genomics data. It stores different kinds of downstream processed data from multiple samples in a single database. A powerful search interface allows to dynamically filter the data to be displayed with respect to different criteria. The combination of AJAX technology and a fast visualization engine facilitates a highly dynamic visualization for large amounts of data. FISH Oracle 2 is able to simultaneously display different data sets, thus simplifying their comparison. Filter and display options can be changed on the fly. High quality image export enables the life scientist to easily communicate the results, e.g. in presentations or publications. A comprehensive data administration assures to keep track of the data stored in the database.

Proper citation: FISH Oracle (RRID:SCR_010927) Copy   

•   Source: SciCrunch Registry

https://omictools.com/l2l-tool

THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone.. Documented on August 26, 2019.

Database of published microarray gene expression data, and a software tool for comparing that published data to a user''''s own microarray results. It is very simple to use - all you need is a web browser and a list of the probes that went up or down in your experiment. If you find L2L useful please consider contributing your published data to the L2L Microarray Database in the form of list files. L2L finds true biological patterns in gene expression data by systematically comparing your own list of genes to lists of genes that have been experimentally determined to be co-expressed in response to a particular stimulus - in other words, published lists of microarray results. The patterns it finds can point to the underlying disease process or affected molecular function that actually generated the observed changed in gene expression. Its insights are far more systematic than critical gene analyses, and more biologically relevant than pure Gene Ontology-based analyses. The publications included in the L2L MDB initially reflected topics thought to be related to Cockayne syndrome: aging, cancer, and DNA damage. Since then, the scope of the publications included has expanded considerably, to include chromatin structure, immune and inflammatory mediators, the hypoxic response, adipogenesis, growth factors, hormones, cell cycle regulators, and others. Despite the parochial origins of the database, the wide range of topics covered will make L2L of general interest to any investigator using microarrays to study human biology. In addition to the L2L Microarray Database, L2L contains three sets of lists derived from Gene Ontology categories: Biological Process, Cellular Component, and Molecular Function. As with the L2L MDB, each GO sub-category is represented by a text file that contains annotation information and a list of the HUGO symbols of the genes assigned to that sub-category or any of its descendants. You don''''t need to download L2L to use it to analyze your microarray data. There is an easy-to-use web-based analysis tool, and you have the option of downloading your results so you can view them at any time on your own computer, using any web browser. However, if you prefer, the entire L2L project, and all of its components, can be downloaded from the download page. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

Proper citation: L2L Microarray Analysis Tool (RRID:SCR_013440) Copy   

•   Source: SciCrunch Registry

http://www.genesigdb.org

Database of traceable, standardized, annotated gene signatures which have been manually curated from publications that are indexed in PubMed. The Advanced Gene Search will perform a One-tailed Fisher Exact Test (which is equivalent to Hypergeometric Distribution) to test if your gene list is over-represented in any gene signature in GeneSigDB. Gene expression studies typically result in a list of genes (gene signature) which reflect the many biological pathways that are concurrently active. We have created a Gene Signature Data Base (GeneSigDB) of published gene expression signatures or gene sets which we have manually extracted from published literature. GeneSigDB was creating following a thorough search of PubMed using defined set of cancer gene signature search terms. We would be delighted to accept or update your gene signature. Please fill out the form as best you can. We will contact you when we get it and will be happy to work with you to ensure we accurately report your signature. GeneSigDB is capable of providing its functionality through a Java RESTful web service.

Proper citation: GeneSigDB (RRID:SCR_013275) Copy   

•   Source: SciCrunch Registry

http://toc.lbg.ac.at/en/research-program/project-tumor-bank

As a basis for the experimental cluster projects, and for further future projects a collection of various biological specimens of cancer patients shall be established. All participating Ludwig Boltzmann Institutes (LBIs) are supplying biological specimens from tumor patients and clinical documentation. At the LBI for Gynecology and Gynecologic Oncology a tumor bank for biological specimens from gynecologic cancer patients already exists. All the procedures for sample processing and storage are well established. Existing equipment for storing tissue specimens at -196 degrees C can be used. Materials from the following malignant diseases are collected: Breast cancer Colorectal cancer Neuroendocrine tumors (NET) (Small cell lung cancer (SCLC) and Carcinoid tumors) Types of biological materials: Tissue (fresh frozen) Bone marrow Blood (serum/plasma/cell fractions) Pleural effusions Ascitic fluids Sputum Bronchial lavage Stool The biological specimens are initially processed at the respective LBIs or at their connected lab facilities. Enrichment of blood samples for disseminated tumor cells is done at the LBI for Gynecology and Gynecologic oncology. Long time storage of all materials is done at appropriate temperatures at the same institution. This LBI also coordinates the logistics. All relevant sample-specific and clinical data are surveyed at the respective LBIs and stored centralized in an on-line data bank in anonymized form, respecting all relevant regulations on data protection and security.

Proper citation: Ludwig Boltzman Tumour Bank (RRID:SCR_004322) Copy   

•   Source: SciCrunch Registry

http://www.bionet.umn.edu/tpf/home.html

Procure and distribute human tissue and other biological samples in support of basic, translational, and clinical cancer research at the University of Minnesota. The TPF is a centralized resource with standardized patient consent, sample collection, processing, storage, quality control, distribution, and electronic record maintenance. Since the 1996 inception of the TPF, over 61,000 tissue samples including well-preserved samples of malignant and benign tumors, organ-matched normal tissue, and other types of diseased tissues, have been collected from surgical specimens obtained at the University of Minnesota Medical Center-Fairview (UMMC-F) University Campus. Surgical pathologists are intellectually engaged in TPF functions, providing researchers with specimen-oriented medical consultation to facilitate research productivity. Prior to surgery, TPF personnel identify and consent patients for procurement of tissue, blood, urine, saliva, and ascites fluid. Within the integrated working environment of the surgical pathology laboratory, freshly obtained tissues not needed for diagnosis are selected and provided by pathologists to TPF personnel. Tissue samples are then assigned an independent code and processed. TPF staff can also work with researchers to individualize the procurement of tissues to fit specific research needs.

Proper citation: University of Minnesota Tissue Procurement Facility (RRID:SCR_004270) Copy   

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http://www.uab.edu/medicine/tcbf/tpsf-sidebar

The Tissue Procurement Shared Facility (TPSF) of the Comprehensive Cancer Center operates as a prospective service to collect, from UAB associated hospitals, normal, malignant, benign, and diseased fresh human tissues and fluids which are then preserved appropriate to protocol. The TPSF can provide normal, malignant, benign, or diseased remnant human tissues and/or fluids from surgical resections, autopsies, or clinical procedures for IRB-approved researchers. The preservation can include fresh storage in media or saline, snap-frozen storage in liquid nitrogen, freezing in OCT for frozen section preparation, or preservation in a fixative of choice. The TPSF can also provide procurement of control tissues including uninvolved tissues or matched tissues from patients with benign disease processes. The histology laboratory can provide paraffin blocks and/or stained or unstained slides. In addition, investigators can obtain access to rare tissues through the national Cooperative Human Tissue Network (CHTN). Although the facility operates as a prospective service specializing in the preparation of samples to protocol, limited banked frozen and paraffin-embedded samples may be available. Investigators are required to complete an application and provide a copy of their IRB approval as well as a brief description of the project for which the requested samples will be utilized. Samples are provided for research purposes only. Processing fees are to offset processing costs and should be included in all grant applications.

Proper citation: UAB Comprehensive Cancer Center Tissue Procurement Shared Facility (RRID:SCR_004222) Copy   

•   Source: SciCrunch Registry

http://www.georgiacancer.org/res-tissue.php

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013.
The Georgia Cancer Specimen and Tissue Bank is committed to a safe and reliable supply of tissue and cell products for research purposes. Work has begun already to build the state tumor bank initiative with operating sites in several locations through the state. We are confident that our results will yield a strong program that will benefit all Georgians and contribute to significant advances in cancer research and knowledge.

Proper citation: Biorepository Alliance of Georgia for Oncology (RRID:SCR_004184) Copy   

•   Source: SciCrunch Registry

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.azcc.arizona.edu/research/shared-services/tacmass/tissue-acquisition

TACMASS collects, preserves, and banks biospecimens obtained from Arizona Cancer Center surgical patients who are seen by University Medical Center surgeons and oncologists. Biospecimens collected at the time of surgery include fresh surgical tissue, blood and urine. Serum, plasma and genomic DNA are harvested from the whole blood. AZCC Members and collaborators may request the use of banked biospecimens through TACMASS. The patient's surgeon or oncologist is responsible for consenting the patient for submission of surgical specimens to the AZCC BioRepository (IRB #06-0609-04, Setsuko Chambers, PI). The surgeon and the Department of Pathology attending physicians and residents are responsible for identifying appropriate tissue for banking that will not compromise pathological diagnosis. Tumor and/or normal adjacent tissue, identified by gross examination, that will not be needed for pathological diagnosis are preserved by fixing in formalin, snap freezing, and/or fixing in RNALater. Histological diagnosis is rendered on each piece of formalin-fixed and snap frozen tissue by Hematoxylin and Eosin staining (H&E). Everyone involved in submitting specimens to the Tumor Bank must maintain a current CITI Certification.

Proper citation: Arizona Cancer Center Tumor Bank (RRID:SCR_003544) Copy   

•   Source: SciCrunch Registry

http://www.cancer.duke.edu/modules/TissueProcurement29/index.php?id=1

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. Over 10,000 patient consents, 5,000 banking events, and 40,000 biospecimens have been processed to date with storage of both formalin fixed paraffin embedded (FFPE) tissue and frozen tissue located within multiple freezers spanning temperatures in the range of -80 degrees to -180 degrees C depending on protocol requirements. Considerable effort continues to be expended to assure compliance with IRB, NIH and HIPAA best practices and guidelines on banking human tissues. The biorepository in place today is the result of the combined efforts of the Duke Cancer Institute (DCI) Breast SPORE, DCI Shared Resource for Tissue and Blood Procurement, and the Duke University School of Medicine Research Foundation (DUSOM-RF). The DCI and the School of Medicine Research Foundation (SOMRF) have funded the collection of frozen and fixed tissues, both malignant and benign, under an ?????????????????excess tissue????????????????? protocol that utilizes freshly excised tissue that is available for research after the needs of the pathologic workup are met. This program procures tissues from many anatomic sites including breast. Recently Duke''s Institute of Genome Science & Policy (IGSP), under the direction of Drs. Geoff Ginsburg and Tom Burke, initiated a blood collection program that spans several departments and institutes. The Breast SPORE blood collection program served as the pilot for this much larger effort. The Breast SPORE tissue and blood collection effort utilizes much of the same infrastructure and personnel that are also supported by the DCI, SOMRF, and IGSP.

Proper citation: DCI Tissue and Blood Procurement Shared Resource (RRID:SCR_004116) Copy   

•   Source: SciCrunch Registry

http://www.nsabp.pitt.edu/NSABP_Pathology.asp

The NSABP (National Surgical Adjuvant Breast and Bowel Project) Tissue Bank is the central repository of tissue samples (stained and unstained slides, tissue blocks, and frozen tissue specimens) collected from clinical trials conducted by the NSABP. The main scientific aim of the NSABP Division of Pathology is to develop clinical context-specific prognostic markers and predictive markers that predict response to or benefit from specific therapeutic modality. To achieve this aim, the laboratory collects the tumor and adjacent normal tissues from cancer patients enrolled into the NSABP trials through its membership institutions, and maintain these valuable materials with clinical follow-up information and distribute them to qualified approved investigators. Currently, specimens from more than 90,000 cases of breast and colon cancer are stored and maintained at the bank. Paraffin embedded tumor specimens are available from NSABP trials. We currently do not bank frozen tissues. All blocks are from patients enrolled in prospective NSABP treatment protocols and complete clinical follow up information as well as demographic information is available. Depending on the project, unstained tissue sections of 4-micrometer thickness, tissue microarrays, or stained slides are provided to the investigators in a blinded study format. Any investigators with novel projects that conform to the research goals of NSABP may apply for the tissue. Please refer to the NSABP Tissue Bank Policy to determine if your project conforms to these goals. Priority is given to NSABP membership institutions who regularly submit tissue blocks.

Proper citation: National Surgical Adjuvant Breast and Bowel Project Tissue Bank (RRID:SCR_004506) Copy   

•   Source: SciCrunch Registry

https://moffitt.org/research-science/shared-resources/tissue/

A central tissue repository at Moffitt specializing in protocol-driven human tissue collection, storage, processing and dissemination. Tissue Core provides investigators with access to high quality, well-annotated human specimens obtained from representative of the patient populations. The advent of powerful molecular technologies has opened the door to developing more effective treatments of patients with cancer. Access to high quality specimens with associated clinical, treatment, recurrence outcome data will be critical to developing and validating the tests needed for diagnosis and prediction of response to therapy. Since its commencement in 1993, the Tissue Core has collected more than 8,000 cases of human liquid cancers and solid primary and metastatic tumors both malignant and benign with adjacent normal, from variety of sites and diagnoses. Collected samples are mostly remnant tissues obtained from patients undergoing therapeutic surgical procedures at the Center. The core also ensures tissue release compliance with USF-IRB and Privacy Board recommendations. * Protocol driven sample collection, processing and distribution * Collection of sample and patient demographic information. * Nucleic acid extractions from tissue sections, FNA, core biopsies blood and bone marrow. * Histology services: H&E slides, staining, sectioning, paraffin blocks, OCT blocks, sample microdissection * WBC, plasma and serum isolation. * Project development and support: Facility staff provides advice and guidance to researchers.

Proper citation: Moffitt Cancer Center Tissue Core (RRID:SCR_004406) Copy   

•   Source: SciCrunch Registry

http://www.tumorbank.org/index.php

Since 1995 the Tumorbank Basel Foundation (German: Stiftung Tumorbank Basel) is a non-for-profit foundation acting in cancer translation research. The purpose of the Tumorbank Basel Foundation is to support in promoting optimization of decision making process for the management of solid cancer personalized treatment modalities to the benefit of the patient. Our Aims: * Acquisition and storage of biological material and clinical data of patients suffering of solid cancer diseases in particular breast and prostate cancer. * Promoting and supporting cancer research using the acquired material and data for clinical studies and translational research. * The development of molecular tumor analyses / tools for cancer patients and the performance of the resulting diagnostic services for personalized treatment modalities. The Tumorbank Basel Foundation has acquired * Data about more than 10''000 breast cancer patients * Data comprise clinical and pathological (histology & IHC) characteristics and biochemical (continuous quantified protein expression levels) features, which are available for almost all samples as well as clinical follow-ups now available for more than 2''000 patients * The RNA expression level of 65 genes has been assessed in >800 samples by Real-Time PCR (317 retrospectively in cases with follow-up, the remaining on a routine basis, prospectively since 2004) The Tumorbank Basel Foundation is storing in Freezers at - 80 degrees C * Ca. 6''000 fresh frozen tissue samples of breast cancer patients * Ca. 9''000 particulate fractions (cytosol / membrane) of all samples analyzed * Ca. 1''000 paired non-malignant adjacent tissue material samples * More than 1''000 extracted RNA samples of good quality * Serum and plasma collection from patients has been started since 2005 All data are stored in a relational SQL data bank using an application. The Tumorbank Basel Foundation is collaborating with several pathology institutes allowing to perform studies correlating results obtained from fresh frozen and paired paraffin embedded tissue samples. The Tumorbank Basel Foundation has started a prostate carcinoma project in Collaboration with the ZeTuP (www.zetup.ch) and pathology institute of St. Gallen. Fresh frozen samples of more than 150 prostate carcinoma patients have been collected and are under investigation.

Proper citation: Tumorbank Basel Foundation (RRID:SCR_004962) Copy   

•   Source: SciCrunch Registry