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http://www.wicell.org/

A nonprofit organization offering research and clinical grade pluripotent stem cell lines, cytogenetic testing, quality control testing and cell banking services to researchers worldwide. The organization is focused on enhancing and expanding the study of human pluripotent stem cells by supporting basic research; establishing research protocols; creating and distributing cell lines; providing training to scientists worldwide; and supporting efforts to unlock the therapeutic potential of stem cell technologies. As home to the Wisconsin International Stem Cell (WISC) Bank, and previously the first US National Stem Cell Bank, WiCell serves the worldwide scientific stem cell community through banking, characterization, and distribution of stem cell lines as well as providing technical support. WiCell also offers cytogenetic services, quality control testing services and clinical grade cell lines to researchers across the globe.

Proper citation: WiCell Research Institute (RRID:SCR_004364) Copy   

•   Source: SciCrunch Registry

http://stemcellcommons.org/

Open source environment for sharing, processing and analyzing stem cell data bringing together stem cell data sets with tools for curation, dissemination and analysis. Standardization of the analytical approaches will enable researchers to directly compare and integrate their results with experiments and disease models in the Commons. Key features of the Stem Cell Commons * Contains stem cell related experiments * Includes microarray and Next-Generation Sequencing (NGS) data from human, mouse, rat and zebrafish * Data from multiple cell types and disease models * Carefully curated experimental metadata using controlled vocabularies * Export in the Investigation-Study-Assay tabular format (ISA-Tab) that is used by over 30 organizations worldwide * A community oriented resource with public data sets and freely available code in public code repositories such as GitHub Currently in development * Development of Refinery, a novel analysis platform that links Commons data to the Galaxy analytical engine * ChIP-seq analysis pipeline (additional pipelines in development) * Integration of experimental metadata and data files with Galaxy to guide users to choose workflows, parameters, and data sources Stem Cell Commons is based on open source software and is available for download and development.

Proper citation: Stem Cell Commons (RRID:SCR_004415) Copy   

•   Source: SciCrunch Registry

http://www.brainarchitecture.org/mouse-home

An atlas project whose goal is to enerate brainwide maps of inter-regional neural connectivity that specify the inputs and outputs of every brain region, at a "mesoscopic" level of analysis. A 3D injection viewer is used to view the mouse brain. To determine the outputs of a brain region, anterograde tracers are used which are taken up by neurons locally ("the input"), then transported actively down the axons to the "output regions." The whole brain is then sliced thinly, and each slice is digitally imaged. These 2-D images are reconstructed in 3D. The majority of the resulting 3-D brain image is unlabeled. Only the injected region and its output regions have tracer in them, allowing for identification of this small fraction of the connectivity map. This procedure is repeated identically, to account for individual variability. To determine the inputs to the same brain region as above, a retrograde tracer is injected in the same stereotaxic location ("the input"), and the process is repeated. In order to accumulate data from different mice (each of whom has a slightly different brain shape and size), 3-D spatial normalization is performed using registration algorithms. These gigapixel images of whole-brain sections can be zoomed to show individual neurons and their processes, providing a "virtual microscope." Each sampled brain is represented in about 500 images, each image showing an optical section through a 20 micron-thick slice of brain tissue. A multi-resolution viewer permits users to journey through each brain, following the pathways taken through three-dimensional brain space by tracer-labeled neuronal pathways. A key point is that at the mid-range "mesoscopic" scale, the team expects to assemble a picture of connections that are stereotypical and probably genetically determined in a species-specific manner. By dividing the volume of a hemisphere of the mouse brain into 250 equidistant, predefined grid-points, and administering four different kinds of tracer injections at each grid point -- in different animals of the same sex and age a complete wiring diagram that will be stitched together in "shotgun" fashion from the full dataset.

Proper citation: Mouse Brain Architecture Project (RRID:SCR_004683) Copy   

•   Source: SciCrunch Registry

http://www.jax.org/index.html

An independent, nonprofit organization focused on mammalian genetics research to advance human health. Their mission is to discover the genetic basis for preventing, treating, and curing human disease, and to enable research for the global biomedical community. Jackson Laboratory breeds and manages colonies of mice as resources for other research institutions and laboratories, along with providing software and techniques. Jackson Lab also conducts genetic research and provides educational material for various educational levels.

Proper citation: Jackson Laboratory (RRID:SCR_004633) Copy   

•   Source: SciCrunch Registry

https://www.facebase.org/content/ocdm

To satisfy the need for standardized terminologies several ontologies, we are developing the Ontology of Craniofacial Development and Malformation. When complete, this ontology will describe several realms of anatomy and development relevant to FaceBase, including: * Human craniofacial anatomy, including developmental progressions * Craniofacial malformations * Mouse craniofacial anatomy * Mappings between mouse and human anatomy These ontologies are currently undergoing active development. As a result, these files should be considered very preliminary. They may not work correctly, and contents will almost certainly undergo significant change. Five (sub) ontologies in this zip archive correspond to the categories described above. * OCDM - Ontology of Craniofacial Development and Malformation: currently imports the CHO, CMO, and the CHMMO. * CHO - Craniofacial Human Ontoloogy: normal adult human craniofacial anatomy derived from the FMA. * CMO - Craniofacial Mouse Ontology: normal adult mouse craniofacial anatomy * CHMMO - Craniofacial Human-Mouse Mapping Ontology: mappings of classes in the * CHO to related (homologous) structures in the CMO. CFMO - Craniofacial Malformation Ontology: abnormal human anatomy, includes the CHO All ontologies are in Protege Frames format (requires Protege 3.x). Ontologies refer to other ontologies via the Protege include mechanism. The CHMMO includes the CHO and the CMO. The OCDM (which is the umbrella ontology) includes all of the rest. Future releases will include translations to the OWL language.

Proper citation: OCDM - Ontology of Craniofacial Development and Malformation (RRID:SCR_005999) Copy   

•   Source: SciCrunch Registry

http://www.brain-map.org/api/index.html

API and demo application for accessing the Allen Brain Atlas Mouse Brain data. Data available via the API includes download high resolution images, expression data from a 3D volume, 3D coordinates of the Allen Reference Atlas, and searching genes with similar gene expression profiles using NeuroBlast. Data made available includes: * High resolution images for gene expression, connectivity, and histology experiments, as well as annotated atlas images * 3-D expression summaries registered to a reference space for the Mouse Brain and Developing Mouse Brain * Primary microarray results for the Human Brain and Non-Human Primate * RNA sequencing results for the Developing Human Brain * MRI and DTI files for Human Brain The API consists of the following resources: * RESTful model access * Image download service * 3-D expression summary download service * Differential expression search services * NeuroBlast correlative searches * Image-to-image synchronization service * Structure graph download service

Proper citation: Allen Brain Atlas API (RRID:SCR_005984) Copy   

•   Source: SciCrunch Registry

http://mango.adult-neurogenesis.de

Database of genes concerning adult neurogenesis mapped to cell types and processes that have been curated from the literature. In its present state, the database is restricted to neurogenesis in the hippocampus.

Proper citation: Mammalian Adult Neurogenesis Gene Ontology (RRID:SCR_006176) Copy   

•   Source: SciCrunch Registry

https://pb.apf.edu.au/phenbank/homePage.html

The NHMRC Australian PhenomeBank (APB) is a non-profit repository of mouse strains used in Medical Research. The database allows you to search for murine strains, housed or archived in Australia, carrying mutations in particular genes, strains with transgenic alterations and for mice with particular phenotypes. 1876 publicly available strains, 922 genes, 439 transgenes The APB has two roles: Provide and maintain a central database of genetically modified mice held in Australia either live or as cryopreserved material; Establish and maintain a mouse strain archive. Strains are archived as cryopreserved sperm or embryos.

Proper citation: NHMRC Australian PhenomeBank (RRID:SCR_006149) Copy   

•   Source: SciCrunch Registry

https://www.infrafrontier.eu/emma/

Non-profit repository for the collection, archiving (via cryopreservation) and distribution of relevant mutant strains essential for basic biomedical research. Users may browse by strain, gene, phenotype, or human disease. Its primary objective is to establish and manage a unified repository for maintaining medically relevant mouse mutants and making them available to the scientific community. Therefore, EMMA archives mutant strains and distributes them to requesting researchers. EMMA also hosts courses in cryopreservation, to promote the use and dissemination of frozen embryos and spermatozoa. Dissemination of knowledge is further fostered by a dedicated resource database. Anybody who wants their mutant mouse strains cryopreserved may deposit strains with EMMA. However depositors must be aware that these strains become freely available to other researchers after being deposited.With more than 8400 mutant mouse strains and asmall but increasing number of rat mutant strains available, EMMA is the primary mouse repository in Europe and the third largest non-profit repository worldwide.

Proper citation: European Mouse Mutant Archive (RRID:SCR_006136) Copy   

•   Source: SciCrunch Registry

http://www.fimre.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 7, 2022. Federation of International Mouse Resources (FIMRe) is a collaborating group of Mouse Repository and Resource Centers worldwide whose collective goal is to archive and provide strains of mice as cryopreserved embryos and gametes, ES cell lines, and live breeding stock to the research community. Goals of the Federation of International Mouse Resources: * Coordinate repositories and resource centers to: ** archive valuable genetically defined mice and ES cell lines being created worldwide ** meet research demand for these genetically defined mice and ES cell lines * Establish consistent, highest quality animal health standards in all resource centers * Provide genetic verification and quality control for genetic background and mutations * Provide resource training to enhance user ability to utilize cryopreserved resources

Proper citation: Federation of International Mouse Resources (RRID:SCR_006137) Copy   

•   Source: SciCrunch Registry

http://www.stembase.ca

A publicly accessible database containing data on Affymetrix DNA microarray experiments, and Serial Analysis of Gene Expression, mostly on human and mouse stem cell samples and their derivatives to facilitate the discovery of gene functions relevant to stem cell control and differentiation. It has grown in both size and scope into a system with analysis tools that examine either the whole database at once, or slices of data, based on tissue type, cell type or gene of interest. There is currently more than 210 stem cell samples in 60 different experiments, with more being added regularly. The samples were originated by researchers of the Stem Cell Network and processed at the Core Facility of Stemcore Laboratories under the management of Ms. Pearl Campbell in the frame of the Stem Cell Genomics Project. Periodically, new expression data is submitted to the Gene Expression Omnibus (GEO) repository at the National Center for Biotechnological Information, in order to allow researchers to compare the data deposited in StemBase to a large amount of gene expression data sets. StemBase is different from GEO in both focus and scope. StemBase is concerned exclusively with stem cell related data. we are focused in Stem Cell research. We have made a significant effort to ensure the quality and consistency of the data included. This allows us to offer more specialized analysis tools related to Stem Cell data. GEO is intended as a large scale public archive. Deposition in a public repository such as GEO is required by most important scientific journals and it is advantageous for a further diffusion of the data since GEO is more broadly used than StemBase.

Proper citation: StemBase (RRID:SCR_006252) Copy   

•   Source: SciCrunch Registry

http://www.mousephenotype.org/impress

Contains standardized phenotyping protocols essential for the characterization of mouse phenotypes. IMPReSS holds definitions of the phenotyping Pipelines and mandatory and optional Procedures and Parameters carried out and data collected by international mouse clinics following the protocols defined. This allows data to be comparable and shareable and ontological annotations permit interspecies comparison which may help in the identification of phenotypic mouse-models of human diseases. The IMPC (International Mouse Phenotyping Consortium) core pipeline describes the phenotype pipeline that has been agreed by the research institutions. IMPReSS has a SOAP web service machine interface. The WSDL can be accessed here: http://www.mousephenotype.org/impress/soap/server?wsdl

Proper citation: Impress (RRID:SCR_006160) Copy   

•   Source: SciCrunch Registry

https://syllabus.med.unc.edu/courseware/embryo_images/

Tutorial that uses scanning electron micrographs (SEMs) as the primary resource to teach mammalian embryology. The 3-D like quality of the micrographs coupled with selected line drawings and minimal text allow relatively easy understanding of the complex morphological changes that occur in utero. Because early human embryos are not readily available and because embryogenesis is very similar across mammalian species, the majority of micrographs that are utilized in this tutorial are of mouse embryos. The remainder are human. This tutorial is divided into units that may be studied in any order. All of the images have a legend that indicates the age of the embryo. If it is a mouse embryo, the approximate equivalent human age is indicated. To minimize labeling, color-coding is widely used. To view the micrographs without color, the cursor may be placed on the image. The SEMs used in this tutorial are from the Kathleen K. Sulik collection. The line drawings have been used with permission from Lippincott Williams & Wilkins and are from the 6th and 7th editions of Langman''s Medical Embryology by T.W. Sadler.

Proper citation: Embryo Images Normal and Abnormal Mammalian Development (RRID:SCR_006297) Copy   

•   Source: SciCrunch Registry

http://www.alzforum.org/

A community building portal dedicated to understanding Alzheimer's disease and related disorders, it reports on the latest scientific findings from basic research to clinical trials, creates and maintains public databases of essential research data and reagents, and produces discussion forums to promote debate, speed the dissemination of new ideas, and break down barriers across disciplines.

Proper citation: Alzheimer's Research Forum (RRID:SCR_006416) Copy   

•   Source: SciCrunch Registry

http://www.informatics.jax.org/searches/GO_form.shtml

With the MGI GO Browser, you can search for a GO term and view all mouse genes annotated to the term or any subterms. You can also browse the ontologies to view relationships between terms, term definitions, as well as the number of mouse genes annotated to a given term and its subterms. The MGI GO browser directly accesses the GO data in the MGI database, which is updated nightly. Platform: Online tool

Proper citation: MGI GO Browser (RRID:SCR_006489) Copy   

•   Source: SciCrunch Registry

http://www.informatics.jax.org/expression.shtml

Community database that collects and integrates the gene expression information in MGI with a primary emphasis on endogenous gene expression during mouse development. The data in GXD are obtained from the literature, from individual laboratories, and from large-scale data providers. All data are annotated and reviewed by GXD curators. GXD stores and integrates different types of expression data (RNA in situ hybridization; Immunohistochemistry; in situ reporter (knock in); RT-PCR; Northern and Western blots; and RNase and Nuclease s1 protection assays) and makes these data freely available in formats appropriate for comprehensive analysis. There is particular emphasis on endogenous gene expression during mouse development. GXD also maintains an index of the literature examining gene expression in the embryonic mouse. It is comprehensive and up-to-date, containing all pertinent journal articles from 1993 to the present and articles from major developmental journals from 1990 to the present. GXD stores primary data from different types of expression assays and by integrating these data, as data accumulate, GXD provides increasingly complete information about the expression profiles of transcripts and proteins in different mouse strains and mutants. GXD describes expression patterns using an extensive, hierarchically-structured dictionary of anatomical terms. In this way, expression results from assays with differing spatial resolution are recorded in a standardized and integrated manner and expression patterns can be queried at different levels of detail. The records are complemented with digitized images of the original expression data. The Anatomical Dictionary for Mouse Development has been developed by our Edinburgh colleagues, as part of the joint Mouse Gene Expression Information Resource project. GXD places the gene expression data in the larger biological context by establishing and maintaining interconnections with many other resources. Integration with MGD enables a combined analysis of genotype, sequence, expression, and phenotype data. Links to PubMed, Online Mendelian Inheritance in Man (OMIM), sequence databases, and databases from other species further enhance the utility of GXD. GXD accepts both published and unpublished data.

Proper citation: Gene Expression Database (RRID:SCR_006539) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/

Consortium that puts sequences into a chromosome context and provides the best possible reference assembly for human, mouse, and zebrafish via FTP. Tools to facilitate the curation of genome assemblies based on the sequence overlaps of long, high quality sequences.

Proper citation: Genome Reference Consortium (RRID:SCR_006553) Copy   

•   Source: SciCrunch Registry

http://www.informatics.jax.org/mgihome/GXD/gxdgen.shtml

A unified resource that combines text-based and 3D graphical methods to store, display, and analyze mouse developmental gene expression information. The Mouse Gene Expression Information Resource resource will integrate the following components: * Gene Expression Database (GXD) - Integrates different types of expression data and provides links to many other resources to place the data into the larger biological and analytical context. * Anatomy Database - Provides the standard nomenclature for developmental anatomy. * 3D Atlas / Graphical Gene Expression Database - Provides a high-resolution digital representation of mouse anatomy reconstructed from serial sections of single embryos at each representative developmental stage enabling 3D graphical display and analysis of in situ expression data.

Proper citation: Mouse Genome Informatics: The Mouse Gene Expression Information Resource Project (RRID:SCR_006630) Copy   

•   Source: SciCrunch Registry

http://www.innatedb.com

Publicly available database of the genes, proteins, experimentally-verified interactions and signaling pathways involved in the innate immune response of humans, mice and bovines to microbial infection. The database captures coverage of the innate immunity interactome by integrating known interactions and pathways from major public databases together with manually-curated data into a centralized resource. The database can be mined as a knowledgebase or used with the integrated bioinformatics and visualization tools for the systems level analysis of the innate immune response. Although InnateDB curation focuses on innate immunity-relevant interactions and pathways, it also incorporates detailed annotation on the entire human, mouse and bovine interactomes by integrating data (178,000+ interactions & 3,900+ pathways) from several of the major public interaction and pathway databases. InnateDB also has integrated human, mouse and bovine orthology predictions generated using Ortholgue software. Ortholgue uses a phylogenetic distance-based method to identify possible paralogs in high-throughput orthology predictions. Integrated human and mouse conserved gene order and synteny information has also been determined to provide further support for orthology predictions. InnateDB Capabilities: * View statistics for manually-curated innate immunity relevant molecular interactions. New manually curated interactions are submitted weekly. * Search for genes and proteins of interest. * Search for experimentally-verified molecular interactions by gene/protein name, interaction type, cell type, etc. * Search genes/interactions belonging to 3,900 pathways. * Visualize interactions using an intuitive subcellular localization-based layout in Cerebral. * Upload your own list of genes along with associated gene expression data (from up to 10 experimental conditions) to interactively analyze this data in a molecular interaction network context. Once you have uploaded your data, you will be able to interactively visualize interaction networks with expression data overlaid; carry out Pathway, Gene Ontology and Transcription Factor Binding Site over-representation analyses; construct orthologous interaction networks in other species; and much more. * Access curated interaction data via a dedicated PSICQUIC webservice.

Proper citation: InnateDB (RRID:SCR_006714) Copy   

•   Source: SciCrunch Registry

http://mouseNET.princeton.edu

A functional network for laboratory mouse based on integration of diverse genetic and genomic data. It allows the users to accurately predict novel functional assignments and network components. MouseNET uses a probabilistic Bayesian algorithm to identify genes that are most likely to be in the same pathway/functional neighborhood as your genes of interest. It then displays biological network for the resulting genes as a graph. The nodes in the graph are genes (clicking on each node will bring up SGD page for that gene) and edges are interactions (clicking on each edge will show evidence used to predict this interaction). Most likely, the first results to load on the results page will be a list of significant Gene Ontology terms. This list is calculated for the genes in the biological network created by the mouseNET algorithm. If a gene ontology term appears on this list with a low p-value, it is statistically significantly overrepresented in this biological network. The graph may be explored further. As you move the mouse over genes in the network, interactions involving these genes are highlighted.If you click on any of the highlighted interactions graph, evidence pop-up window will appear. The Evidence pop-up lists all evidence for this interaction, with links to the papers that produced this evidence - clicking these links will bring up the relevant source citation(s) in PubMed.

Proper citation: MouseNET (RRID:SCR_003357) Copy   

•   Source: SciCrunch Registry