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https://irp.drugabuse.gov/OTTC/rats.php

Core facility and data repository which creates and characterizes transgenic rats for use in models of neurological diseases, such as addiction and neurodegeneration. Researchers can request strain(s) from RRRC or go to the Transgenic Rat Request page.

Proper citation: Optogenetics and Transgenic Technology Core (RRID:SCR_014785) Copy   

•   Source: SciCrunch Registry

http://corefacilities.case.edu/animal.php

A set of core facilities of Case Western Reserve University School of Medicine which allows users to create and analyze in vivo animal models. The various facilities provide animal care, transgenic models, imaging, irradiation, and phenotyping for research concerning such topics as cancer, metabolic processes, and behavior. In vivo animals provided include mice, zebrafish, and rodents.

Proper citation: CWRU In Vivo Animal Facilities (RRID:SCR_014209) Copy   

•   Source: SciCrunch Registry

http://diabetesresearchcenter.dom.wustl.edu/translational-diagnostics-core/

Core provides range of assays for human and animal hormones, peptides, and metabolites related to metabolic disorders.

Proper citation: Washington University School of Medicine Diabetes Research Center Translational Diagnostics Core (RRID:SCR_015161) Copy   

•   Source: SciCrunch Registry

http://drtc.bsd.uchicago.edu/islet-cell-biology-core-about/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 7,2024. Core which provides services and hands-on training in the isolation and functional characterization of pancreatic islets from normal and diabetic humans and mice. It also maintains a repository of insulinoma cell lines for distribution. It puts emphasis on facilitating studies of primary islet cells and it has developed many unique tools and techniques for carrying such studies including novel animals models, biophysical methods and a library of adenovirus-based expression constructs for studying beta-cell function.

Proper citation: University of Chicago Diabetes Research and Training Center Islet Cell Biology Core (RRID:SCR_015132) Copy   

•   Source: SciCrunch Registry

http://livercenter.yale.edu/core-facilities/cellular-molecular-physiology-core-facility.aspx

Core facility that provides technical expertise, equipment and personnel to Liver Center Investigators who wish to work with animal models of liver disease, isolated liver cells, or gene expression in liver tissue. The Cell Isolation sub-core isolates hepatocytes and non-parenchymal liver cells primarily from rat and mouse, while the Molecular Biology sub-core provides equipment and expertise to Liver Center members in a centralized facility.

Proper citation: Yale Liver Center Cellular and Molecular Physiology Core (RRID:SCR_015258) Copy   

•   Source: SciCrunch Registry

http://appris.bioinfo.cnio.es/

A database that houses annotations of human splice isoforms. It adds reliable protein structural and functional data and information from cross-species conservation. A visual representation of the annotations for each gene allows users to easily identify functional changes brought about by splicing events. In addition to collecting, integrating and analyzing reliable predictions of the effect of splicing events, it also selects a single reference sequence for each gene, termed the principal isoform, based on the annotations of structure, function and conservation for each transcript.

Proper citation: APPRIS (RRID:SCR_012019) Copy   

•   Source: SciCrunch Registry

http://compartments.jensenlab.org/Downloads

Web resource that integrates evidence on protein subcellular localization from manually curated literature, high-throughput screens, automatic text mining, and sequence-based prediction methods. All evidence is mapped to common protein identifiers and Gene Ontology terms, and further unify it by assigning confidence scores that facilitate comparison of the different types and sources of evidence and visualize these scores on a schematic cell.

Proper citation: COMPARTMENTS Subcellular localization database (RRID:SCR_015561) Copy   

•   Source: SciCrunch Registry

https://www.tfcheckpoint.org/

Collection of transcription factors annotated according to experimental and other evidence on their function as true DbTFs. Provides reference for both small scale experiments and genome scale studies. Curated compendium of specific DNA-binding RNA polymerase II transcription factors.

Proper citation: tfcheckpoint (RRID:SCR_023880) Copy   

•   Source: SciCrunch Registry

http://www.civm.duhs.duke.edu/

Biomedical technology research center dedicated to the development of novel imaging methods for the basic scientist and the application of the methods to important biomedical questions. The CIVM has played a major role in the development of magnetic resonance microscopy with specialized MR imaging systems capable of imaging at more than 500,000x higher resolution than is common in the clinical domain. The CIVM was the first to demonstrate MR images using hyperpolarized 3He which has been moved from mouse to man with recent clinical trials performed at Duke in collaboration with GE. More recently the CIVM has developed the molecular imaging workbench---a system dedicated to multimodality cardiopulmonary imaging in the rodent. Their collaborators are employing these unique imaging systems in an extraordinary range of mouse and rat models of neurologic disease, cardiopulmonary disease and cancer to illuminate the underlying biology and explore new therapies.

Proper citation: Center for In Vivo Microscopy (RRID:SCR_001426) Copy   

•   Source: SciCrunch Registry

http://www.norc.uab.edu/corefacilities/animalmodels

Core that provides specialized expertise in the use of animal models and instrumentation to facilitate animal research related to nutrition and obesity.

Proper citation: University of Alabama at Birmingham Nutrition and Obesity Research Center Animal Models Core (RRID:SCR_015466) Copy   

•   Source: SciCrunch Registry

http://amp.pharm.mssm.edu/lib/chea.jsp

Data analysis service for gene-list enrichment analysis against a manual database. It allows users to input lists of mammalian gene symbols for which the program computes over-representation of transcription factor targets from the ChIP-X database. The database integrates interaction data from ChIP-chip, ChIP-seq, ChIP-PET and DamID studies and contains 189,933 interactions, manually extracted from 87 publications, describing the binding of 92 transcription factors to 31,932 target genes.

Proper citation: ChEA (RRID:SCR_005403) Copy   

•   Source: SciCrunch Registry

http://smd.stanford.edu/cgi-bin/source/sourceSearch

SOURCE compiles information from several publicly accessible databases, including UniGene, dbEST, UniProt Knowledgebase, GeneMap99, RHdb, GeneCards and LocusLink. GO terms associated with LocusLink entries appear in SOURCE. The mission of SOURCE is to provide a unique scientific resource that pools publicly available data commonly sought after for any clone, GenBank accession number, or gene. SOURCE is specifically designed to facilitate the analysis of large sets of data that biologists can now produce using genome-scale experimental approaches Platform: Online tool

Proper citation: SOURCE (RRID:SCR_005799) Copy   

•   Source: SciCrunch Registry

http://www.ideal.force.cs.is.nagoya-u.ac.jp/IDEAL/

IDEAL, Intrinsically Disordered proteins with Extensive Annotations and Literature, is a collection of knowledge on experimentally verified intrinsically disordered proteins (IDPs) or intrinsically disordered regions (IDRs). IDEAL contains manually curated annotations on IDPs in locations, structures, and functional sites such as protein binding regions and posttranslational modification sites together with references and structural domain assignments. Protean segment One of the unique phenomena seen in IDPs is so-called the coupled folding and binding, where a short flexible segment can bind to its binding partner with forming a specific structure to act as a molecular recognition element. IDEAL explicitly annotates these regions as protean segment (ProS) when unstructured and structured information are both available in the region. Access to the data All the entries are tabulated in the list and individual entries can be retrieved by using the search tool at the upper-right corner in this page. IDEAL also provides the BLAST search, which can find homologs in IDEAL. All the information in IDEAL can be downloaded in the XML file.

Proper citation: IDEAL - Intrinsically Disordered proteins with Extensive Annotations and Literature (RRID:SCR_006027) Copy   

•   Source: SciCrunch Registry

http://www.pathbase.net/

Database of histopathology photomicrographs and macroscopic images derived from mutant or genetically manipulated mice. The database currently holds more than 1000 images of lesions from mutant mice and their inbred backgrounds and further images are being added continuously. Images can be retrieved by searching for specific lesions or class of lesion, by genetic locus, or by a wide set of parameters shown on the Advanced Search Interface. Its two key aims are: * To provide a searchable database of histopathology images derived from experimental manipulation of the mouse genome or experiments conducted on genetically manipulated mice. * A reference / didactic resource covering all aspects of mouse pathology Lesions are described according to the Pathbase pathology ontology developed by the Pathbase European Consortium, and are available at the site or on the Gene Ontology Consortium site - OBO. As this is a community resource, they encourage everyone to upload their own images, contribute comments to images and send them their feedback. Please feel free to use any of the SOAP/WSDL web services. (under development)

Proper citation: Pathbase (RRID:SCR_006141) Copy   

•   Source: SciCrunch Registry

http://edwardslab.bmcb.georgetown.edu/downloads/

The Peptide Sequence Database contains putative peptide sequences from human, mouse, rat, and zebrafish. Compressed to eliminate redundancy, these are about 40 fold smaller than a brute force enumeration. Current and old releases are available for download. Each species'' peptide sequence database comprises peptide sequence data from releveant species specific UniGene and IPI clusters, plus all sequences from their consituent EST, mRNA and protein sequence databases, namely RefSeq proteins and mRNAs, UniProt''s SwissProt and TrEMBL, GenBank mRNA, ESTs, and high-throughput cDNAs, HInv-DB, VEGA, EMBL, IPI protein sequences, plus the enumeration of all combinations of UniProt sequence variants, Met loss PTM, and signal peptide cleavages. The README file contains some information about the non amino-acid symbols O (digest site corresponding to a protein N- or C-terminus) and J (no digest sequence join) used in these peptide sequence databases and information about how to configure various search engines to use them. Some search engines handle (very) long sequences badly and in some cases must be patched to use these peptide sequence databases. All search engines supported by the PepArML meta-search engine can (or can be patched to) successfully search these peptide sequence databases.

Proper citation: Peptide Sequence Database (RRID:SCR_005764) Copy   

•   Source: SciCrunch Registry

http://www.disgenet.org

Database and discovery platform containing publicly available collections of genes and variants associated to human diseases. Integrates data from curated repositories, GWAS catalogues, animal models and scientific literature.

Proper citation: DisGeNET (RRID:SCR_006178) Copy   

•   Source: SciCrunch Registry

http://www.civm.duhs.duke.edu/neuro2012ratatlas/

Multidimensional atlas of the adult Wistar rat brain based on magnetic resonance histology (MRH). The atlas has been carefully aligned with the widely used Paxinos-Watson atlas based on optical sections to allow comparisons between histochemical and immuno-marker data, and the use of the Paxinos-Watson abbreviation set. Our MR atlas attempts to make a seamless connection with the advantageous features of the Paxinos-Watson atlas, and to extend the utility of the data through the unique capabilities of MR histology: a) ability to view the brain in the skull with limited distortion from shrinkage or sectioning; b) isotropic spatial resolution, which permits sectioning along any arbitrary axis without loss of detail; c) three-dimensional (3D) images preserving spatial relationships; and d) widely varied contrast dependent on the unique properties of water protons. 3D diffusion tensor images (DTI) at what we believe to be the highest resolution ever attained in the rat provide unique insight into white matter structures and connectivity. The 3D isotropic data allow registration of multiple data sets into a common reference space to provide average atlases not possible with conventional histology. The resulting multidimensional atlas that combines Paxinos-Watson with multidimensional MRH images from multiple specimens provides a new, comprehensive view of the neuroanatomy of the rat and offers a collaborative platform for future rat brain studies. To access the atlas, click view supplementary materials in CIVMSpace at the bottom of the following webpage.

Proper citation: Adult Wistar Rat Atlas (RRID:SCR_006288) Copy   

•   Source: SciCrunch Registry

http://wukong.tongji.edu.cn/pepid

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A database to store the curated epigenetic data from studies of prostate cancer retrieved by literature mining. The Prostate Epigenetic Database (PEpiD) is meant as a resource for finding previous studies of prostate cancer in humans, mice and rats. Searches can be targeted through the categories of DNA methylation, histone modification, and microRNA.

Proper citation: PEpiD (RRID:SCR_000235) Copy   

•   Source: SciCrunch Registry

https://bams1.org/connectomes/standard_rat.php, https://bams1.org/connectomes/custom_rat.php

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 9,2022. Database of information about brain region circuitry, it collates data from the literature on tract tracing studies and provides tools for analysis and visualization of connectivity between brain regions., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: BAMS Connectivity (RRID:SCR_000561) Copy   

•   Source: SciCrunch Registry

http://lifespandb.sageweb.org/

Database that collects published lifespan data across multiple species. The entire database is available for download in various formats including XML, YAML and CSV.

Proper citation: Lifespan Observations Database (RRID:SCR_001609) Copy   

•   Source: SciCrunch Registry