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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.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

http://pluto3.nci.nih.gov/tissue/default.cfm

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. The Specimen Resource Locator is a database to help researchers locate human specimens (tissue, serum, DNA/RNA, other specimens) for cancer research. It includes tissue banks and tissue procurement systems with access to normal, benign, precancerous and cancerous human tissue from a variety of organs. Researchers specify the types of specimens, number of cases, preservation methods and associated data they require. The Locator will then search the database and return a list of tissue resources most likely to meet their requirements. When no match is obtained, the researcher is referred to the NCI Tissue Expediter ([email protected]). The Tissue expediter is a scientist who can help researchers identify appropriate resources and/or appropriate collaborators.

Proper citation: NCI Specimen Resource Locator (RRID:SCR_004754) Copy   

•   Source: SciCrunch Registry

https://www.sbpdiscovery.org/biomedical-research/shared-resources/cancer-metabolism

Facility that aims to investigate role of metabolism in cancer on cellular and organismal level, combining in vitro and in vivo analysis. Comprehensive metabolic facility, including stable isotope tracing and flux analysis. Provides analysis of metabolism using specialist instruments and methodologies, together with advice on planning experiments and analyzing data. All instruments and approaches are available on fee-for-service basis to Cancer Center scientists, but alsoto outside users. Samples for most services can be shipped, but Seahorse analyzer users need to be local so they can bring live cells for analysis.

Proper citation: Sanford Burnham Prebys Medical Discovery Institute Cancer Metabolism Core Facility (RRID:SCR_014873) Copy   

•   Source: SciCrunch Registry

http://www.salk.edu/science/core-facilities/integrative-genomics-and-bioinformatics-core/

Core facility established to assist the Salk community with integrating genomics data into their research. The primary focus of the core is to provide analysis support for next-generation sequencing applications.

Proper citation: Salk Institute Razavi Newman Integrative Genomics and Bioinformatics Core Facility (IGC) (RRID:SCR_014842) Copy   

•   Source: SciCrunch Registry

https://www.med.upenn.edu/cbica/captk/

Software platform for analysis of radiographic cancer images. Used as quantitative imaging analytics for precision diagnostics and predictive modeling of clinical outcome.

Proper citation: Cancer Imaging Phenomics Toolkit (RRID:SCR_017323) Copy   

•   Source: SciCrunch Registry

https://github.com/caleblareau/mgatk

Software python-based command line interface for processing .bam files with mitochondrial reads and generating high-quality heteroplasmy estimation from sequencing data. This package places a special emphasis on mitochondrial genotypes generated from single-cell genomics data, primarily mtscATAC-seq, but is generally applicable across other assays.

Proper citation: mgatk (RRID:SCR_021159) Copy   

•   Source: SciCrunch Registry

https://github.com/humanlongevity/HLA

Software tool for fast and accurate HLA typing from short read sequence data. Iteratively refines mapping results at amino acid level to achieve four digit typing accuracy for both class I and II HLA genes, taking only 3 min to process 30× whole genome BAM file on desktop computer.

Proper citation: xHLA (RRID:SCR_022277) Copy   

•   Source: SciCrunch Registry

https://github.com/RabadanLab/arcasHLA

Software tool for high resolution HLA typing from RNAseq. Fast and accurate in silico inference of HLA genotypes from RNA-seq.

Proper citation: arcasHLA (RRID:SCR_022286) Copy   

•   Source: SciCrunch Registry

http://cancer.osu.edu/research/cancerresearch/sharedresources/ltb/Pages/index.aspx

The OSU Comprehensive Cancer Center Leukemia Tissue Bank Shared Resource (LTBSR) facilitates the successful translation of basic leukemia research to the clinical setting via an extensive repository of tissue samples and accompanying pathologic, cytogenetic and clinical data for ready correlation of clinical and biological results. The LTBSR, which is an NCI-sponsored biorepository, has more than 40,000 vials of cryopreserved viable cells and 13,000 vials of matched frozen plasma and/or serum samples from more than 4,000 patients treated for leukemia and other malignancies. Committed to furthering translational research efforts for OSUCCC - James members and the cancer research community, the LTBSR provides investigators with training and technical support as well as procurement, processing, storage, retrieval and distribution of clinical research materials. In many cases, the LTBSR serves as the central processing lab for multi-site trials in which the principal investigator is an OSUCCC - James member. The LTBSR's goals are to: * Provide a central collection, processing and a state-of-the-art repository for samples collected from leukemia patients treated on OSUCCC - James protocols, and * Provide materials to investigators involved in collaborative studies with OSU, who examine relevant cellular and molecular properties of leukemia and correlate these properties with clinical or population-based outcomes.

Proper citation: Ohio State Leukemia Tissue Bank (RRID:SCR_000529) Copy   

•   Source: SciCrunch Registry

http://www.cpctr.net/

THIS RESOURCE IS NO LONGER IN SERVICE. Doumented on September 23,2022. The National Cancer Institute initially established the Cooperative Prostate Cancer Tissue Resource (CPCTR) to provide prostate cancer tissue samples with clinical annotation to researchers. The Resource provides access to formalin-fixed, paraffin-embedded primary prostate cancer tissue with associated clinical and follow-up data for research studies, particularly studies focused on translating basic research findings into clinical application. Fresh-frozen tissue is also available with limited clinical follow up information since these are more recent cases. The Resource database contains pathologic and clinical information linked to a large collection of prostate tissue specimens that is available for research. Researchers can determine whether the Resource has the tissues and patient data they need for their individual research studies. Consultation and interpretive services: Assistance is available from trained CPCTR pathologists. The CPCTR can provide consultative assistance in staining interpretation, and scoring, on a collaborative basis. Fresh Frozen and Paraffin Tissue: The resource has over 7,000 annotated cases (including 7,635 specimens and 38,399 annotated blocks). Tissue Microarrays (TMA): The CPCTR has slides from prostate cancer TMAs with associated clinical data. The information provided for each case on the arrays (derived from radical prostatectomy specimens) includes: age at diagnosis, race, PSA at diagnosis, tumor size, TNM stage, Gleason score and grade, and vital status and other variables.

Proper citation: CPCTR: Cooperative Prostate Cancer Tissue Resource (RRID:SCR_000803) Copy   

•   Source: SciCrunch Registry

http://cbbiweb.uthscsa.edu/KMethylomes/

Datbase and web-based system for visualization and analysis of genome-wide methylation data of human cancers.

Proper citation: Cancer Methylome System (RRID:SCR_012013) Copy   

•   Source: SciCrunch Registry

http://www.cravat.us/

A web-based application designed with an easy-to-use interface to facilitate the high-throughput assessment and prioritization of genes and missense alterations important for cancer tumorigenesis.

Proper citation: CRAVAT (RRID:SCR_012776) Copy   

•   Source: SciCrunch Registry

https://www.gem-beta.org/Public/Home.aspx

Database that contains behavioral and social science measures organized by theoretical constructs. GEM is designed to enable researchers to use common measures with the goal of exchanging harmonized data.

Proper citation: Grid-Enabled Measures Database (RRID:SCR_016043) Copy   

•   Source: SciCrunch Registry

https://rtips.cancer.gov/rtips/index.do

Database of cancer control interventions and program materials. It is designed to provide program planners and public health practitioners easy and immediate access to research-tested materials.

Proper citation: Research-tested Intervention Programs (RTIPs) (RRID:SCR_016042) Copy   

•   Source: SciCrunch Registry

https://www.clinicalgenome.org

Genomics knowledgebase for clinical relevance of genes and variants for use in research. ClinGen's primary function is to store and share information for the benefit of the scientific community. Laboratory scientists, clinicians, and patients can share and access data.

Proper citation: ClinGen (RRID:SCR_014968) Copy   

•   Source: SciCrunch Registry

https://pancreatlas.org/

Collection of human pancreas data and images. Platform to share data from human pancreas samples. Houses reference datasets from human pancreas samples, achieved through generosity of organ donors and their families.

Proper citation: Pancreatlas (RRID:SCR_018567) Copy   

•   Source: SciCrunch Registry

https://www.mdanderson.org/research/research-resources/core-facilities/functional-proteomics-rppa-core.html

Core provides technology for functional proteomics studies and centralized, standardized and quality controlled services locally and globally.

Proper citation: RPPA Core Facility (RRID:SCR_016649) Copy   

•   Source: SciCrunch Registry

https://www.mdanderson.org/research/research-resources/core-facilities/proteomics-facility.html

Facility provides mass spectrometry analysis of proteins. Provides access to mass spectrometry based proteomics technologies and services including Protein Identification, Molecular Weight Determination, Quantitative Protein Analysis, Post-translational Modification Analysis, LC or LC-MS Analysis, Equipment Usage, Additional Data Analysis:Bioinformatics, statistics, pathway analysis and Assistance preparing materials for manuscripts or grants.Consultations for custom assays for other MS Services are also available.

Proper citation: University of Texas MD Anderson Cancer Center Proteomics Core Facility (RRID:SCR_017731) Copy   

•   Source: SciCrunch Registry

https://voices.uchicago.edu/ucflow/

Core offers services in cytometry and antibody technology, helps to design projects, data acquisition, analysis and/or interpretation beyond routine practices,critical drafting and/or revision of manuscript for intellectual content purposes.

Proper citation: Chicago University Cytometry and Antibody Technology Core Facility (RRID:SCR_017760) Copy   

•   Source: SciCrunch Registry