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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   

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http://www.uchicagoddrcc.org

Center whose goals include fostering collaboration among basic and clinical investigators, facilitating the use of new technologies in the study of treatment of digestive diseases, and providing education and training for improved treatment and diagnosis.

Proper citation: University of Chicago Digestive Diseases Research Core Center (RRID:SCR_015601) Copy   

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http://www.bsc.gwu.edu/dpp/index.htmlvdoc

Multicenter clinical research study aimed at discovering whether modest weight loss through dietary changes and increased physical activity or treatment with the oral diabetes drug metformin (Glucophage) could prevent or delay the onset of type 2 diabetes in study participants. At the beginning of the DPP, all 3,234 study participants were overweight and had blood glucose levels higher than normal but not high enough for a diagnosis of diabetesa condition called prediabetes. In addition, 45 percent of the participants were from minority groups-African American, Alaska Native, American Indian, Asian American, Hispanic/Latino, or Pacific Islander-at increased risk of developing diabetes. The DPP found that participants who lost a modest amount of weight through dietary changes and increased physical activity sharply reduced their chances of developing diabetes. Taking metformin also reduced risk, although less dramatically. In the DPP, participants from 27 clinical centers around the United States were randomly divided into different treatment groups. The first group, called the lifestyle intervention group, received intensive training in diet, physical activity, and behavior modification. By eating less fat and fewer calories and exercising for a total of 150 minutes a week, they aimed to lose 7 percent of their body weight and maintain that loss. The second group took 850 mg of metformin twice a day. The third group received placebo pills instead of metformin. The metformin and placebo groups also received information about diet and exercise but no intensive motivational counseling. A fourth group was treated with the drug troglitazone (Rezulin), but this part of the study was discontinued after researchers discovered that troglitazone can cause serious liver damage. The participants in this group were followed but not included as one of the intervention groups. In the years since the DPP was completed, further analyses of DPP data continue to yield important insights into the value of lifestyle changes in helping people prevent type 2 diabetes and associated conditions. For example, one analysis confirmed that DPP participants carrying two copies of a gene variant, or mutation, that significantly increased their risk of developing diabetes benefited from lifestyle changes as much as or more than those without the gene variant. Another analysis found that weight loss was the main predictor of reduced risk for developing diabetes in DPP lifestyle intervention group participants. The authors concluded that diabetes risk reduction efforts should focus on weight loss, which is helped by increased exercise.

Proper citation: Diabetes Prevention Program (RRID:SCR_001501) Copy   

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http://tiger.bsc.es

Resource enables integrative exploration of genetic and epigenetic basis of development of Type 2 Diabetes, together with other associated functional, molecular and clinical data, centered in biology and role of pancreatic beta cells.The gene expression regulatory variation landscape of human pancreatic islets.

Proper citation: TIGER Data Portal (RRID:SCR_023626) Copy   

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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   

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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   

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https://huttenhower.sph.harvard.edu/picrust/

Software for predicting functional abundances based only on marker gene sequences.Used for prediction of metagenome functions. Contains updated and larger database of gene families and reference genomes, provides interoperability with any operational taxonomic unit (OTU)-picking or denoising algorithm, and enables phenotype predictions. Allows addition of custom reference databases.

Proper citation: PICRUSt2 (RRID:SCR_022647) Copy   

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https://medschool.cuanschutz.edu/diabetes-research-center

Center to facilitate diabetes research at University of Colorado by integrating interdisciplinary basic, translational, and clinical diabetes research base; providing infrastructure and resources that are indispensable for continued discovery and progress towards diabetes research and developing improved prediction and disease prevention;providing P&F and enrichment programs to support DRC investigators and their trainees, and recruit new and young investigators into diabetes research.

Proper citation: University of Colorado Diabetes Research Center (RRID:SCR_022897) Copy   

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https://ncdiabetesresearch.org/

Interactive regional diabetes research community across four premiere research institutions in North Carolina, who currently garner over $70 million annually for support of their diabetes research: Duke University (Duke), The University of North Carolina at Chapel Hill (UNC), Wake Forest School of Medicine (WF), and North Carolina A&T State University (NC A&T State). NCDRC supports Research Cores that represent unique strengths at each institution.

Proper citation: North Carolina Diabetes Research Center (RRID:SCR_022896) Copy   

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http://www.cristudy.org/Chronic-Kidney-Disease/Chronic-Renal-Insufficiency-Cohort-Study/

A prospective observational national cohort study poised to make fundamental insights into the epidemiology, management, and outcomes of chronic kidney disease (CKD) in adults with intended long-term follow up. The major goals of the CRIC Study are to answer two important questions: * Why does kidney disease get worse in some people, but not in others? * Why do persons with kidney disease commonly experience heart disease and stroke? The CRIC Scientific and Data Coordinating Center at Penn receives data and provides ongoing support for a number of Ancillary Studies approved by the CRIC Cohort utilizing both data collected about CRIC study participants as well as their biological samples. The CRIC Study has enrolled over 3900 men and women with CKD from 13 recruitment sites throughout the country. Following this group of individuals over the past 10 years has contributed to the knowledge of kidney disease, its treatment, and preventing its complications. The NIDDKwill be extending the study for an additional 5 years, through 2018. An extensive set of study data is collected from CRIC Study participants. With varying frequency, data are collected in the domains of medical history, physical measures, psychometrics and behaviors, biomarkers, genomics/metabolomics, as well as renal, cardiovascular and other outcomes. Measurements include creatinine clearance and iothalamate measured glomerular filtration rate. Cardiovascular measures include blood pressure, ECG, ABI, ECHO, and EBCT. Clinical CV outcomes include MI, ischemic heart disease-related death, acute coronary syndromes, congestive heart failure, cerebrovascular disease, peripheral vascular disease, and composite outcomes. The CRIC Study has delivered in excess of 150,000 bio-samples and a dataset characterizing all 3939 CRIC participants at the time of study entry to the NIDDKnational repository. The CRIC Study will also be delivering a dataset to NCBI''''s Database for Genotypes and Phenotypes.

Proper citation: Chronic Renal Insufficiency Cohort Study (RRID:SCR_009016) Copy   

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https://hddc.hms.harvard.edu/gnotobiotics-microbiology-and-metagenomics

Core facility that assists investigators evaluating host microbiota and its role in normal physiology and disease. It includes a number of resources for groups studying the role of the microbiota in human health and disease.

Proper citation: Harvard Digestive Diseases Center Biomedical CORE D: Gnotobiotic Mice, Microbiology and Metagenomics (RRID:SCR_012319) Copy   

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http://sph.unc.edu/norc/norc-diet-and-physical-activity-core/

Core that provides diet, physical activity, or statistical analysis consultation, as well as consultation for the design and development of diet and physical activity data collection protocols.

Proper citation: University of North Carolina at Chapel Hill Nutrition and Obesity Research Center Diet and Physical Activity Core (RRID:SCR_012588) Copy   

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https://einsteinmed.edu/centers/diabetes-research/research-areas/biomedical-cores/translational-research-core/index.html

Core services include consultation, technical support and training and mentoring in clinical and translational research methods that are specifically applicable to diabetes, its complications and related metabolic disorders. Personel provides expertise in first-in-human and mechanistic studies in integrative physiology, in clinical trials of diabetes and obesity, and in application of new technologies.

Proper citation: Einstein-Mount Sinai Diabetes Research Center Translational Research Core Facility (RRID:SCR_015068) Copy   

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http://drc.ucsf.edu/mouse-metabolism-core

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 10,2024. Core which provides technical support for UCSF investigators to conduct metabolic studies using a 12-chambered Comprehensive Lab Animal Monitoring System (CLAMS), an EchoMRI, and Dual energy X-ray absorptiometry, which together allow measurement of food intake, water intake, motor activities, core temperature, and body composition in live mice. It also helps to identify emerging technologies that will enhance multiple research programs and coordinates the acquisition and maintenance of those facilities.

Proper citation: University of California San Francisco Diabetes Research Center Mouse Metabolism Core (RRID:SCR_015101) Copy   

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https://www.baderc.org/cores/cbmcore/

Services provided include tissue preparation, embedding and sectioning for electron microscopy, use of electron microscope and photography of thin sections, immunogold staining for electron microscopy, preparation and incubation of samples (cells and tissues) for immunofluorescence microscopy, confocal microscopy and digital imaging.

Proper citation: Boston Area Diabetes Endocrinology Research Center Cell Biology and Morphology Core Facility (RRID:SCR_015069) Copy   

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https://diabetes.ucsf.edu/drc-islet

Core that enables clinical and basic research that analyzes the function of isolated pancreatic islets. It coordinates and delivers purified human islets to investigators when research need matches the availability of a human pancreas.

Proper citation: University of California San Francisco Diabetes Research Center Islet Production Core Facility (RRID:SCR_015106) Copy   

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https://diabetes.ucsf.edu/drc-microscopy

Core that consolidates, enhances and disseminates Diabetes Center resources and expertise in tissue and cell imaging technologies. Confocal fluorescence, widefield fluorescence, high throughput fluorescence and brightfield microscopes are available directly within the DRC Microscopy Core. Image quantification and analysis is performed at dedicated workstations.

Proper citation: University of California San Francisco Diabetes Research Center Microscopy Core Facility (RRID:SCR_015103) Copy   

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http://drc.ucsf.edu/lentiviral-rnai-core

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 5,2024. Core that provides reagents, equipment, training, supervision, and monitoring of investigators wishing to ensure the proper compliance with biosafety containment required for lentiviral-based research, lentiviral preparation services for investigators, and education on RNAi experimentation, through the lentiviral core website, and through protocols available at the facility.

Proper citation: University of California San Francisco Diabetes Research Center Lentiviral RNAi Core Facility (RRID:SCR_015104) Copy   

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http://www.baderc.org/cores/molbioCore.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 24,2024. Core that provides services for DNA sequencing and oligonucleotide synthesis, as well as support for projects that require research laboratory automation, such as siRNA screens and transcript abundance profiling. It also offers experimental design and advice for automation and high throughput screening of siRNA collections based on the Ambion siRNA collection.

Proper citation: Boston Area Diabetes Endocrinology Research Center Molecular Biology (RRID:SCR_015079) Copy   

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http://www.uab.edu/shp/drc/animal-physiology-core-links

Core that provides diabetes researches with diabetes related phenotyping in small animal models. Their services offered include the assessment of body composition, energy balance, glucose homeostasis, cardiovascular assessment, imaging, and transgenic animals models.

Proper citation: University of Alabama at Birmingham Diabetes Research Center Animal Physiology Core Facility (RRID:SCR_015110) Copy   

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