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https://motrpac-data.org/

National research consortium designed to discover and perform preliminary characterization of range of molecular transducers that underlie effects of physical activity in humans. Used to study molecular changes that occur during and after exercise and to advance understanding of how physical activity improves and preserves health. Six year program into mechanisms of how physical activity improves health and prevents disease led by NIH Office of Strategic Coordination, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institute of Diabetes and Digestive and Kidney Diseases, National Institute on Aging, and National Institute of Biomedical Imaging and Bioengineering.

Proper citation: MoTrPAC Data Hub (RRID:SCR_017611) Copy   

•   Source: SciCrunch Registry

https://portal.hubmapconsortium.org/

Data portal as part of Human BioMolecular Atlas Program. Data available on HuBMAP Portal is open access data to be used for research of human biology. Certain data types with potential for re-identification are available in restricted access either directly through this portal by login-dependent permissions or through dbGAP. All data users are expected to respect privacy and confidentiality of donors who provided samples. Data are not to be used to re-identify donors or their family members without further approval from HuBMAP. Data for single-cell, three-dimensional maps of various human tissues. Data include discrete, complex organs (kidney, ureter, bladder, lung, breast, small intestine and colon); distributed organ systems (vasculature); systems comprising dynamic or motile cell types with distinct microenvironments (lymphatic organs: spleen, thymus, and lymph nodes).

Proper citation: HuBMAP Data Portal (RRID:SCR_021703) Copy   

•   Source: SciCrunch Registry

http://www.stanford.edu/group/nolan/retroviral_systems/phx.html

A second-generation retrovirus producer lines for the generation of helper free ecotropic and amphotropic retroviruses. The lines are based on the 293T cell line (a human embryonic kidney line transformed with adenovirus E1a and carrying a temperature sensitive T antigen co-selected with neomycin). The unique feature of this cell line is that it is highly transfectable with either calcium phosphate mediated transfection or lipid-based transfection protocols-- up to 50% or higher of cells can be transiently transfected. The lines were created by placing into 293T cells constructs capable of producing gag-pol, and envelope protein for ecotropic and amphotropic viruses. The lines offered advantages over previous stable systems in that virus can be produced in just a few days. Academic and non-profit laboratories may obtain the Phoenix cells from either Allele Biotechnology or the National Gene Vector Bank. The vectors may be obtained from Addgene. They are no longer distributing these reagents from the lab.

Proper citation: Phoenix (RRID:SCR_003163) 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

http://www.ndriresource.org/NDRI_Initiatives/HBDI/36/

Database of medical history and genealogical data on over 6700 families who are affected by type 1 diabetes and a repository of DNA and immortalized cell lines collected from 500 families. This database and repository was originally created to help researchers uncover the genetic causes of type 1 diabetes but today, it is also used by researchers who study type 2 diabetes, diabetic complications, autoimmune diseases, kidney disease, and other disorders. The following resources and services are available to researchers through HBDI: * International Type 1 Diabetes Database: This database includes more than 6700 families with diabetes, related complications and other genetic diseases. There are extensive genealogical and medical histories for more than 90,000 individuals. NDRI conducts searches of the database for approved research requests. * HBDI Catalog: The catalog contains 503 family pedigrees with associated cell lines, DNA, and serum for research. Also available are HLA-typing and auto-antibody test results for diabetes families in the catalog. * HBDI Repository: The HBDI repository contains cell lines, DNA, and HLA typing information from 480 families, and frozen buffy coats from 23 families, all with Type 1 diabetes. They have recently expanded the repository to include specimens from individuals with rare diseases. * Customized Collections: NDRI will collect data from patients and physicians, conduct phone interviews and collect blood and other specimens for research on request., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Human Biological Data Interchange (RRID:SCR_004591) Copy   

•   Source: SciCrunch Registry

http://jsu.eagle-i.net/i/0000012c-1c64-7caa-a830-7bcf80000000

The JHS is the largest single-site longitudinal, population-based, cohort study of 5,302 persons initiated in the fall of 2000 to prospectively investigate the determinants of CVD among African Americans in the Jackson, MS metropolitan statistical area. The JHS investigates the various genotype and phenotype factors that affect high blood pressure, heart disease, strokes, diabetes and other important diseases in African Americans. The primary objective of the Jackson Heart Study is to investigate the causes of cardiovascular disease (CVD) in African Americans to learn how to best prevent this group of diseases in the future. More specific objectives include: 1. Identification of factors, which influence the development, and worsening of CVD in African Americans, with an emphasis on manifestations related to high blood pressure (such as remodeling of the left ventricle of the heart, coronary artery disease, heart failure, stroke and disorders affecting the blood vessels of the kidney). 2. Building research capabilities in minority institutions at the undergraduate and graduate level by developing partnerships between minority and majority institutions and enhancing participation of minority investigators in large-scale epidemiologic studies. 3. Attracting minority students to and preparing them for careers in health sciences.

Proper citation: Jackson Heart Study (RRID:SCR_009902) Copy   

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http://amedeo.com/

A service created to allow healthcare professionals to access timely, relevant information within their respective fields. Users can subscribe to receive weekly emails with bibliographic lists about new scientific publications, personal web pages for one-time download of available abstracts, and an overview of the medical literature published in relevant journals over the past 12 to 24 months.

Proper citation: AMEDEO: The Medical Literature Guide (RRID:SCR_002284) Copy   

•   Source: SciCrunch Registry

https://exrna-atlas.org

Software tool as data and metadata repository of Extracellular RNA Communication Consortium. Atlas includes small RNA sequencing and qPCR derived exRNA profiles from human and mouse biofluids. All RNAseq datasets are processed using version 4 of exceRpt small RNAseq pipeline. Atlas accepts submissions for RNAseq or qPCR data.

Proper citation: exRNA Atlas (RRID:SCR_017221) Copy   

•   Source: SciCrunch Registry

https://www.clinicaltrials.gov/study/NCT00360646

Prospective and retrospective registry of well-characterized cases of drug-induced liver disease. The goals of Network include the development of standardized procedures to identify and fully characterize bona fide cases of drug- and complementary and alternative medicines (CAM)-induced liver injury, and to conduct controlled, clinical studies that will include extensive collection of data, serum, DNA, and tissue specimens. Cases of liver injury due to herbal medications are also included. The network will also develop terminology and standardized definitions for DILI, and to develop causality assessment instruments that are sensitive, specific, and reproducible. DILIN is funded by a cooperative agreement and includes five clinical centers and a central data coordinating center. The research goals of DILIN are to: * Create a registry of carefully documented DILI cases * Identify clinical, immunological, and environmental risk factors for drug- and CAM-mediated hepatotoxicity * Create a bank of biological specimens consisting of DNA, plasma, and immortalized lymphocytes to facilitate detailed genetic analyses * Characterize the natural history of drug- and CAM-induced DILI for at least six months following enrollment * Develop the capability to recontact these individuals over an extended period of time so that additional studies exploring DILI mechanisms can be performed Two studies are being initiated by the network. In the Retrospective Study, the implicated drugs are restricted to isoniazid, phenytoin, combination clavulanic acid/amoxicillin, and valproic acid (Depakote), Nitrofurantoin, Trimethoprim-sulfamethoxazole, Minocycline, and Quinolone antibiotics. These drugs were chosen because they are frequently administered to patients not receiving other hepatotoxic drugs, making it easier to establish causality. Patients must be alive, and the date of onset of the DILI episode must be on or after January 1, 1994. In the Prospective Study, all incident cases of drug- and CAM-induced liver injury are being considered. Initial presentation to a healthcare professional must be within the previous six months. A detailed medication history of the implicated DILI drug together with all prescription, OTC, and herbal medications is being recorded. Liver and serological tests are being performed to characterize the injury and to exclude competing causes of liver injury. A blood sample is also being drawn for plasma storage and DNA isolation. These cases will be followed longitudinally to characterize the long-term effects of the DILI episode. For both studies, documented, clinically significant DILI must be recorded in the patient's medical charts so that a causal determination can be made. Patients will be excluded if they are unwilling or unable to provide a blood sample or participate in the genetics component. Children under two years of age at the time of enrollment are excluded due to blood-volume requirements. If you have patients who are eligible to participate in either study, please contact one the DILIN clinical sites. As a general policy, the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) invites investigator-initiated research project applications for ancillary studies to ongoing, large-scale clinical trials, epidemiological studies, and disease databases supported by the Institute. These studies are focused on a wide range of diseases and conditions including diabetes, obesity, acute and chronic liver disease, chronic kidney disease, and benign prostatic hyperplasia, among others.

Proper citation: Drug-Induced Liver Injury Network (RRID:SCR_001524) Copy   

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http://medicine.iupui.edu/neph/obrien/digital

Core facility which develops and implements software and methods of image segmentation for fluorescence microscopy data.

Proper citation: Indiana O'Brien Center for Advanced Microscopic Analysis Digital Image Analysis Core (RRID:SCR_015276) Copy   

•   Source: SciCrunch Registry

http://bioinfo.nist.gov/hmpd/

Database of mitochondrial and human nuclear encoded proteins involved in mitochondrial biogenesis and function. This database consolidates information from SwissProt, LocusLink, Protein Data Bank (PDB), GenBank, Genome Database (GDB), Online Mendelian Inheritance in Man (OMIM), Human Mitochondrial Genome Database (mtDB), MITOMAP, Neuromuscular Disease Center and Human 2-D PAGE Databases. The mitochondrion plays a central role in cellular metabolism, and evidence of mitochondrial involvement in a number of different human diseases is increasing. This database is intended as a tool not only to aid in studying the mitochondrion but in studying the associated diseases. Mitochondrial DNA Sequence: A graphical tool was developed to visualize the human mitochondrial DNA sequences that highlight coding regions for RNAs and proteins. Disease susceptible mutations are also noted in the sequence. Mitochondrial DNA Polymorphism: Human mitochondrial sequences of different ethnic groups were obtained from the Human Mitochondrial Genome Database. A DNA sequence analysis tool was developed to compare polymorphisms of different human mitochondrial DNA sequences. This tool allows the user to select mitochondrial sequences from any two human populations and compare them for sequences variations. Mitochondrial proteins related diseases: Malfunction of mitochondrial proteins affect many cells from brain, heart, liver, skeletal muscles, kidney, and the endocrine and the respiratory systems which lead to many diseases. Relevant information for mitochondrial related diseases from OMIM, the Neuromuscular Disease Center and MITOMAP are gathered, and mitochondrion-associated diseases are grouped, categorized, and linked to OMIM. 3-D Structures of Mitochondrial proteins: The available 3D structures for mitochondrial proteins are presented through a custom-made interface. A concise HTML page is generated for reporting the structural details and the associated information obtained from relevant web sites (PDBREPORT, Interatomic Contacts of Structural Units (CSU), PROCHECK, Ligand Protein Contacts (LPC), PROMOTIF and CastP). References are linked to the PubMed site. The 3-D structures are presented through the use of a Kinemage.

Proper citation: Human Mitochondrial Protein Database (RRID:SCR_002913) Copy   

•   Source: SciCrunch Registry

http://saweb2.sabiosciences.com/manuals/GEArrayBrochure.pdf

THIS RESOURCE HAS BEEN DISCONTINUED, documented April 15, 2016. New GEArray Expression Analysis Suite 2.0 was released at Dec 21, 2006, please read Release Notices for details. SABiosciences' GEArray Analysis Suite uses advanced Java functionality. In order to experience full functionality of this Portal, the following free programs and upgrades for PC and Macs should be properly installed. PC Environment Downloads Browser compatibility is not an issue on Windows systems, so all operating systems running Windows 98 and above and either Internet explorer or Netscape should be fine. Java 1.4.1 or above is required--this should download automatically upon the first entry into the Portal. If this does not happen, Java 1.5 is available for download from the following URL: Java 1.5 Mac Environment Downloads Browser compatibility is an issue, and Mac Operating Systems prior to Panther are not able to fully take advantage of this Portal's functionality. These programs need to be downloaded and installed in a specific order as follows: Panther 10.3.5 (Operating System), Safari 1.2 (Compatible Internet Browser) and Java 1.4.2 (Java environment). Abstract. INTRODUCTION: Toll-like receptors (TLR) comprehend an emerging family of receptors that recognize pathogen-associated molecular patterns and promote the activation of leukocytes. Surgical trauma and ischemia-reperfusion injury are likely to provide exposure to endogenous ligands for TLR in virtually all kidney transplant recipients. METHODS: Macroarray (GEArray OHS-018.2 Series-Superarray) analyses of 128 genes involved in TLR signaling pathway were performed in nephrectomy samples of patients with chronic allograft nephropathy (CAN) and acute rejection (AR, vascular and non vascular). The analysis of each membrane was performed by GEArray Expression Analysis Suite 2.0. RESULTS: Macroarray profile identified a gene expression signature that could discriminate CAN and AR. Three genes were significantly expressed between CAN and vascular AR: Pellino 2; IL 8 and UBE2V1. In relation to vascular and non-vascular AR, there were only two genes with statistical significance: IL-6 and IRAK-3. CONCLUSION: Vascular and non-vascular AR and CAN showed different expression of a few genes in TLR pathway. The analysis of nephrectomy showed that activation of TLR pathway is present in AR and CAN. Sponsor. This work was supported by the inconditional grant from Fundao de Amparo a Pesquisa do Estado de So Paulo (FAPESP, 04/08311-6), from Conselho Nacional de Pesquisa e Desenvolvimento (CNPq) and from Fundao Osvaldo Ramos.

Proper citation: GEArray Expression Analysis Suite 2.0 (RRID:SCR_000282) Copy   

•   Source: SciCrunch Registry

http://specimencentral.com/

World's open biospecimen research database where biobanks and biomedical researchers meet to exchange human biospecimen needs and supply: whole blood, serum, plasma, solid tissue samples and more. The connection is accelerated so researchers save valuable time and money and tissue banks utilize inventory. The pace of specimen procurement remains unacceptably slow to the biomedical research community. Specimen Central is the foremost global resource to aid biomedical researchers in expediting their search for high quality human biospecimens, tissues, samples and specimens. They facilitate your search for blood, whole blood, buccal swab, DNA, RNA, protein, cell lines, plasma, serum, RBC, white cells, buffy coat, fluid, marrow, urine, stem cells, and solid tissue such as tumor, tumor and biopsy materials spanning all manner of common and rare pathologies and indications including Alzheimer's, basal cell carcinoma, bladder cancer, bone cancer, brain cancer, breast cancer, cerebrospinal fluid, amniotic fluid, colorectal cancer, colon cancer, hodgkins and non-hodgkins lymphoma, kidney/renal cancer, leukemia, liver cancer, lung cancer, melanoma, multiple sclerosis, myeloma neuroblastoma, neurodegenerative diseases, ovarian cancer, pancreatic cancer, prostate cancer, urinary cancer. This includes adult and pediatric indications. Specimen Central users specify a number of variables in their Specimen Requests, including preparation, preservation and handling requirements such as cryo-preserved, FFPE (Formalin-fixed paraffin-embedded), formalin, frozen, refrigerated, OCT, snap frozen, paraffin block, fresh, prospective, autopsy or cadaveric, etc. Many users require clinically annotated date associated with their specimens, as well as documentation of IRB or ethics committee approval and informed consents. For Researchers Most specimen databases require researchers to waste time and effort entering lengthy registrations and search queries that yield poor results, if anything. Specimen Central solves this problem by having tissue banks search for you. From years to months, months to weeks, and weeks to days, Specimen Central seeks to reduce delays and costs in the research & development life cycle by expediting connections between demand and supply. For Biobanks The capital costs of maintaining a biobank infrastructure are substantial and growing. Biobanks use Specimen Central as a marketing tool to augment their business development efforts. By routinely checking Specimen Central's Specimen Requests, biobanks can uncover market demand for their inventories and develop new connections and revenue streams to defray costs. Specimen Central supplements - not displaces - the efforts of your sales representatives, agents, brokers and commercial partners.

Proper citation: SpecimenCentral.com (RRID:SCR_003536) Copy   

•   Source: SciCrunch Registry

http://www.lamhdi.org/

THIS RESOURCE IS NO LONGER IN SERVICE, it has been replaced by Monarch Initiative. LAMHDI, the initiative to Link Animal Models to Human DIsease, is designed to accelerate the research process by providing biomedical researchers with a simple, comprehensive Web-based resource to find the best animal model for their research. LAMDHI is a free, Web-based, resource to help researchers bridge the gap between bench testing and human trials. It provides a free, unbiased resource that enables scientists to quickly find the best animal models for their research studies. LAMHDI includes mouse data from MGI, the Mouse Genome Informatics website; zebrafish data from ZFIN, the Zebrafish Model Organism Database; rat data from RGD, the Rat Genome Database; yeast data from SGD, the Saccharomyces Genome Database; and fly data from FlyBase. LAMHDI.org is operational today, and data is added regularly. Enhancements are planned to let researchers contribute their knowledge of the animal models available through LAMHDI. The LAMHDI goal is to allow researchers to share information about and access to animal models so they can refine research and testing, and reduce or replace the use of animal models where possible. LAMHDI Database Search: LAMHDI brings together scientifically validated information from various sources to create a composite multi-species database of animal models of human disease. To do this, the LAMHDI database is prepared from a variety of sources. The LAMHDI team takes publicly available data from OMIM, NCBI''s Entrez Gene database, Homologene, and WikiPathways, and builds a mathematical graph (think of it as a map or a web) that links these data together. OMIM is used to link human diseases with specific human genes, and Entrez provides universal identifiers for each of those genes. Human genes are linked to their counterpart genes in other species with Homologene, and those genes are linked to other genes tentatively or authoritatively using the data in WikiPathways. This preparatory work gives LAMHDI a web of human diseases linked to specific human genes, orthologous human genes, homologous genes in other species, and both human and non-human genes involved in specific metabolic pathways associated with those diseases. LAMHDI includes model data that partners provide directly from their data structures. For instance, MGI provides information about mouse models, including a disease for each model, as well as some genetic information (the ID of the model, in fact, identifies one or more genes). ZFIN provides genetic information for each zebrafish model, but no diseases, so zebrafish models are integrated by using the genes as the glue. For instance, a zebrafish model built to feature the zebrafish PKD2 gene would plug into the larger disease-gene map at the node representing the zebrafish PKD2 gene, which is connected to the node representing the human PKD2 gene, which in turn is connected to the node representing the human disease known as polycystic kidney disease. (Some of the partner data LAMHDI receives can even extend the base map. MGI provides a disease for every model, and in some cases this allows the creation of a disease-to-gene relationship in the LAMHDI database that might not already be documented in the OMIM dataset.) With curatorial and model information in hand, LAMHDI runs a lengthy automated process that exhaustively searches for every possible path between each model and each disease in the data, up to a set number of hops, producing for each disease-to-model pair a set of links from the disease to the model. The algorithm avoids circular paths and paths that include more than one disease anywhere in the middle of the path. At the end of this phase, LAMHDI has a comprehensive set of paths representing all the disease-to-model relationships in the data, varying in length from one hop to many hops. Each disease-to-model path is essentially a string of nodes in the data, where each node represents a disease, a gene, a linkage between genes (an orthologue, a homologue, or a pathway connection, referred to as a gene cluster or association), or a model. Each node has a human-friendly label, a set of terms and keywords, and - in most cases - a URL linking the node to the data source where it originated. When a researcher submits a search on the LAMHDI website, LAMHDI searches for the user''s search terms in its precomputed list of all known disease-to-model paths. It looks for the terms not only in the disease and model nodes, but also in every node along each path. The complete set of hits may include multiple paths between any given disease-to-model pair of endpoints. Each of these disease-to-model pair sets is ordered by the number of hops it involves, and the one involving the fewest hops is chosen to represent its respective disease-to-model pair in the search results presented to the user. Results are sorted by scores that represent their matches. The number of hops is one barometer of the strength of the evidence linking the model and the disease; fewer hops indicates the relationship is stronger, more hops indicates it may be weaker. This indicator works best for comparing models from a single partner dataset: MGI explicitly identifies a disease for each mouse model, so there can be disease-to-model hits for mice that involve just one hop. Because ZFIN does not explicitly identify a disease for each model, no zebrafish model will involve fewer than four hops to the nearest disease, from the zebrafish model to a zebrafish gene to a gene cluster to a human gene to a human disease.

Proper citation: LAMHDI: The Initiative to Link Animal Models to Human DIsease (RRID:SCR_008643) Copy   

•   Source: SciCrunch Registry

http://medschool.umaryland.edu/

Medical school of the University of Maryland, Baltimore and is affiliated with the University of Maryland Medical Center and Medical System. Located in Baltimore City, Maryland, U.S.

Proper citation: University of Maryland School of Medicine; Maryland; USA (RRID:SCR_005837) Copy   

•   Source: SciCrunch Registry

http://www.utsouthwestern.edu/

Public academic health science center in Dallas, Texas.

Proper citation: University of Texas Southwestern Medical Center; Texas; USA (RRID:SCR_011724) Copy   

•   Source: SciCrunch Registry

http://medschool.duke.edu/

Center for medical education, clinical care and biomedical research. Medical education includes programs that train medical students, residents and fellows, research scientists and post-doctoral fellows, physical therapists, physician assistants and pathologist assistants.

Proper citation: Duke University School of Medicine; North Carolina; USA (RRID:SCR_011194) Copy   

•   Source: SciCrunch Registry

http://duke.edu/

Private research university in Durham, North Carolina. Founded by Methodists and Quakers in 1838. Home of Blue Devils, Duke University has undergraduate and graduate students and world class faculty.

Proper citation: Duke University; North Carolina; USA (RRID:SCR_011193) Copy   

•   Source: SciCrunch Registry

http://www.mayoclinic.org/patient-visitor-guide/minnesota

Nonprofit academic medical center based in Rochester, Minnesota, focused on integrated clinical practice, education, and research. Highly specialized in cardiovascular diseases and surgery. Practice specializes in treating difficult cases through tertiary care and destination medicine.

Proper citation: Mayo Clinic Minnesota; Minnesota; USA (RRID:SCR_011386) Copy   

•   Source: SciCrunch Registry

http://medicine.yale.edu/index.aspx

Proper citation: Yale School of Medicine; Connecticut; USA (RRID:SCR_006339) Copy   

•   Source: SciCrunch Registry