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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 1, 2015. Consortium that aims to facilitate interdisciplinary collaborations to advance the understanding of pancreatic islet development and function, with the goal of developing innovative therapies to correct the loss of beta cell mass in diabetes, including cell reprogramming, regeneration and replacement. They are responsible for collaboratively generating the necessary reagents, mouse strains, antibodies, assays, protocols, technologies and validation assays that are beyond the scope of any single research effort. The scientific goals for the BCBC are to: * Use cues from pancreatic development to directly differentiate pancreatic beta cells and islets from stem / progenitor cells for use in cell-replacement therapies for diabetes, * Determine how to stimulate beta cell regeneration in the adult pancreas as a basis for improving beta cell mass in diabetic patients, * Determine how to reprogram progenitor / adult cells into pancreatic beta-cells both in-vitro and in-vivo as a mean for developing cell-replacement therapies for diabetes, and * Investigate the progression of human type-1 diabetes using patient-derived cells and tissues transplanted in humanized mouse models. Many of the BCBC investigator-initiated projects involve reagent-generating activities that will benefit the larger scientific community. The combination of programs and activities should accelerate the pace of major new discoveries and progress within the field of beta cell biology.
Proper citation: Beta Cell Biology Consortium (RRID:SCR_005136) Copy
Ratings or validation data are available for this resource
http://iidp.coh.org/Default.aspx
The goal of the Integrated Islet Distribution Program (IIDP) is to work with the leading islet isolation centers in the U.S. to distribute high quality human islets to the diabetes research community, in order to advance scientific discoveries and translational medicine.
Proper citation: Integrated Islet Distribution Program (IIDP) (RRID:SCR_014387) Copy
http://www.diabetes-translation.org
Centers that are part of an integrated program whose cores support and enhance diabetes type II translation research. The CDTRs aim to enhance the efficiency, productivity, effectiveness and multidisciplinary nature of diabetes translation research.
Proper citation: Centers for Diabetes Translation Research (RRID:SCR_015149) Copy
http://globalprojects.ucsf.edu/project/novel-small-molecule-therapies-cystic-fibrosis
Research center that focuses on developing novel therapies for cystic fibrosis, enhancing research projects examining the mechanisms of the disease, and developing new small-molecule therapies that can be translated into the clinic.
Proper citation: Cystic Fibrosis Center - University of California San Francisco (RRID:SCR_015398) Copy
https://maayanlab.cloud/sigcom-lincs
Web server that serves over million gene expression signatures processed, analyzed, and visualized from LINCS, GTEx, and GEO. Data and metadata search engine for gene expression signatures.
Proper citation: SigCom LINCS (RRID:SCR_022275) Copy
https://github.com/zdk123/SpiecEasi
Software R package for microbiome network analysis. Used for inference of microbial ecological networks from amplicon sequencing datasets. Combines data transformations developed for compositional data analysis with graphical model inference framework that assumes underlying ecological association network is sparse.
Proper citation: SpiecEasi (RRID:SCR_022712) Copy
Repository of biospecimen and phenotype data collected from Crohn's disease and ulcerative colitis cases and controls recruited at six sites throughout North America that are available to the scientific community. Phenotyping is performed using a standardized protocol, and lymphoblastoid cell lines are established for each subject. Phenotype data for each subject are collected by the Consortium's Data Coordinating Center (DCC), and phenotype data for all subjects with DNA samples are available. The resulting DNA samples have already been utilized by the Consortium to complete various association studies, including genome-wide association studies using dense genotyping arrays. Researchers can obtain DNA samples and phenotype, genotype, and pedigree data through the Data Repository. GWAS data must be requested through dbGAP. The IBDGC is involved with independent genetic research studies and actively works with members of the IBD and genetic communities on collaborative projects. They are also members of the International IBD Genetics Consortium. Phenotype Tools: The Consortium Phenotype Committee, led by Dr. Hillary Steinhart designed and validated paper forms to collect extensive phenotype data on Crohn's Disease and ulcerative colitis. Consortium phenotype tools are available for use by non-Consortium members.
Proper citation: NIDDK Inflammatory Bowel Disease Genetics Consortium (RRID:SCR_001461) Copy
Group of 10 academic laboratories provide pancreatic islets of cGMP-quality to eligible investigators for use in FDA approved, IRB-approved transplantation protocols in which isolated human islets are transplanted into qualified patients afflicted with type 1 diabetes mellitus; optimize the harvest, purification, function, storage, and shipment of islets while developing tests that characterize the quality and predict the effectiveness of islets transplanted into patients with diabetes mellitus; and provide pancreatic islets for basic science studies. The centers are electronically linked through an Administrative and Bioinformatics Coordinating Center (ABCC). The ABCC manages a system with objectively defined criteria that establishes the order of priority for islet distribution. It also provides database and other informatics to track the utilization of pancreata and all distributed clinical grade islets for transplant and basic research, and supports the Islet Cell Resource Centers Consortium so that the research community has a single entry point to the program. Qualified researchers from domestic institutions may request islets by submitting a written application to the director of the ABCC. The ICRs will distribute Islets as appropriate for either clinical or basic science protocol use to eligible investigators who have received a favorable review and subsequent approval by the ICR Steering Committee (SC). The Administrative and Bioinformatics Coordinating Center (ABCC) manages the distribution according to a priority list. The ABCC will give preference to investigators who have peer-reviewed, NIH-funded research support.
Proper citation: Islet Cell Resource Centers (RRID:SCR_002806) Copy
http://chgr.mc.vanderbilt.edu/page/gist
Software package to test if a marker can account in part for the linkage signal in its region. There are two versions of the software: Windows and Linux/Unix.
Proper citation: Genotype-IBD Sharing Test (RRID:SCR_006257) Copy
Public global Protein Data Bank archive of macromolecular structural data overseen by organizations that act as deposition, data processing and distribution centers for PDB data. Members are: RCSB PDB (USA), PDBe (Europe) and PDBj (Japan), and BMRB (USA). This site provides information about services provided by individual member organizations and about projects undertaken by wwPDB. Data available via websites of its member organizations.
Proper citation: Worldwide Protein Data Bank (wwPDB) (RRID:SCR_006555) Copy
http://digestive.niddk.nih.gov/statistics/statistics.aspx
A collection of statistics about specific digestive diseases, including prevalence, mortality, care delivery and cost.
Proper citation: Digestive Diseases Statistics for the United States (RRID:SCR_006703) Copy
https://www.atypicaldiabetesnetwork.org/
Portal dedicated to characterizing, discovering and defining rare and atypical forms of diabetes. Network of universities, hospitals and clinics across the United States dedicated to better understanding atypical diabetes. Team of academic institutions and scientists collaborates with physicians and healthcare groups to identify those with atypical diabetes and learn more about their health.
Proper citation: Rare and Atypical Diabetes Network (RRID:SCR_024732) Copy
Web interactive browser to visualize data and perform gene set enrichment analysis along with gene and SNP lookup. Web interface used to query STARNET datasets and downstream analysis which includes RNAseq from 7 tissues: blood, free internal mammary artery (MAM), atherosclerotic aortic root (AOR), subcutaneous fat (SF), visceral abdominal fat (VAF), skeletal muscle (SKLM), and liver (LIV). Paired SNP genotyping data is included and utilized for tissue expression quantitative trait loci (eQTL), CAD heritability (H2), co-expression networks and gene regulatory networks.
Proper citation: STARNET (RRID:SCR_025238) Copy
https://github.com/cafferychen777/ggpicrust2
Software R package for analyzing and interpreting results of PICRUSt2 functional prediction. Offers range of features, including pathway name/description annotations, advanced differential abundance methods, and visualization of differential abundance results. Used for PICRUSt2 predicted functional profile analysis and visualization.
Proper citation: ggpicrust2 (RRID:SCR_025965) Copy
Provides Cincinnati Children s Hospital Medical Center; Cincinnati; Ohio resources in confocal, wide-field, and spatial technique applications.
Proper citation: Cincinnati Children's Hospital Confocal Imaging Core Facility (RRID:SCR_022628) Copy
https://ncdiabetesresearch.org/acsmc
Core to leverage data, patient populations and investigators at each NCDRC institution, including accessing expertise and resources of regional Clinical and Translational Science Institute hubs (Duke, UNC, and Wake Forest). Research navigators in ACSMC provides input and navigation of clinical research resources available to diabetes investigators based on extensive experience in diabetes specific studies and methodology and deep knowledge of NCDRC resources available at each institution.
Proper citation: North Carolina Diabetes Research Center Advanced Clinical Study Methods Core Facility (RRID:SCR_022908) Copy
Provides diabetes researchers at University of Colorado with access to microscopy and mass cytometry systems. Provides expertise and training to use equipment effectively for diabetes related tissues; expertise and validated diabetes related resources to prepare samples appropriately; guidance to design experiments; resources to analyze data; assistance with data interpretation.
Proper citation: University of Colorado Anschutz Medical Campus Diabetes Research Center Cell and Tissue Analysis Core Facility (RRID:SCR_022906) Copy
Provides diabetes researchers with access to novel human stem cell-derived in vitro cell models for investigating cellular and molecular features of both Type 1 and Type 2 diabetes. Recent progress in stem cell, organoid culture, gene editing and directed differentiation technologies has afforded opportunities to develop pre-clinical human models.Provides expertise, infrastructure and access to novel human model systems and technologies to DRC investigators. Provides expertise, resources and training in stem cell technologies together with quality control testing, validation standardization and authentication all model platforms and reagents.
Proper citation: University of Colorado Anschutz Medical Campus Diabetes Research Center Disease Modeling Core Facility (RRID:SCR_022905) Copy
Core leverages current clinical research facilities and equipment available at Barbara Davis Center for Childhood Diabetes, UC AMC Clinical Translational Research Center, University of Colorado Hospital, Denver Veteran Administration Medical Center and Children Hospital Colorado.Core integrates diabetes research across these institutions through communication and distribution of resources available, and creates shared sample and data biobanks and recruiting database of mothers, infants, children, adolescents and adults with diabetes, diabetes risk and controls.
Proper citation: University of Colorado Anschutz Medical Campus Diabetes Research Center Clinical Resource Core Facility (RRID:SCR_022903) Copy
https://github.com/compbiolabucf/PTNet
Graph based learning model for protein expression estimation by considering miRNA-mRNA interactions. Estimates protein levels by considering miRNA-mRNA interaction network, mRNA expression and miRNA expression.
Proper citation: PTNet (RRID:SCR_022975) Copy
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