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http://ratmap.gen.gu.se/

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 September 2, 2016. Database for defining official rat gene symbols. It includes rat gene symbols from three major sources: the Rat Genome Database (RGD), Ensembl, and NCBI-Gene. All rat symbols are compared with official symbols from orthologous human genes as specified by the Human Gene Nomenclature Committee (HGNC). Based on the outcome of the comparisons, a rat gene symbol may be selected. Rat symbols that do not match a human ortholog undergo a strict procedure of comparisons between the different rat gene sources as well as with the Mouse Genome Database (MGD). For each rat gene this procedure results in an unambiguous gene designation. The designation is presented as a status level that accompanies every rat gene symbol suggested in the database. The status level describes both how a rat symbol was selected, and its validity. Rat Gene Symbol Tracker approves rat gene symbols by an automatic procedure. The rat genes are presented with links to RGD, Ensembl, NCBI Gene, MGI and HGNC. RGST ensures that each acclaimed rat gene symbol is unique and follows the guidelines given by the RGNC. To each symbol a status level associated, describing the gene naming process.

Proper citation: Rat Gene Symbol Tracker (RRID:SCR_003261) Copy   

•   Source: SciCrunch Registry

http://bioinfo.mbi.ucla.edu/ASAP/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on 8/12/13. Database to access and mine alternative splicing information coming from genomics and proteomics based on genome-wide analyses of alternative splicing in human (30 793 alternative splice relationships found) from detailed alignment of expressed sequences onto the genomic sequence. ASAP provides precise gene exon-intron structure, alternative splicing, tissue specificity of alternative splice forms, and protein isoform sequences resulting from alternative splicing. They developed an automated method for discovering human tissue-specific regulation of alternative splicing through a genome-wide analysis of expressed sequence tags (ESTs), which involves classifying human EST libraries according to tissue categories and Bayesian statistical analysis. They use the UniGene clusters of human Expressed Sequence Tags (ESTs) to identify splices. The UniGene EST's are clustered so that a single cluster roughly corresponds to a gene (or at least a part of a gene). A single EST represents a portion of a processed (already spliced) mRNA. A given cluster contains many ESTs, each representing an outcome of a series of splicing events. The ESTs in UniGene contain the different mRNA isoforms transcribed from an alternatively spliced gene. They are not predicting alternative splicing, but locating it based on EST analysis. The discovered splices are further analyzed to determine alternative splicing events. They have identified 6201 alternative splice relationships in human genes, through a genome-wide analysis of expressed sequence tags (ESTs). Starting with 2.1 million human mRNA and EST sequences, they mapped expressed sequences onto the draft human genome sequence and only accepted splices that obeyed the standard splice site consensus. After constructing a tissue list of 46 human tissues with 2 million human ESTs, they generated a database of novel human alternative splices that is four times larger than our previous report, and used Bayesian statistics to compare the relative abundance of every pair of alternative splices in these tissues. Using several statistical criteria for tissue specificity, they have identified 667 tissue-specific alternative splicing relationships and analyzed their distribution in human tissues. They have validated our results by comparison with independent studies. This genome-wide analysis of tissue specificity of alternative splicing will provide a useful resource to study the tissue-specific functions of transcripts and the association of tissue-specific variants with human diseases.

Proper citation: ASAP: the Alternative Splicing Annotation Project (RRID:SCR_003415) Copy   

•   Source: SciCrunch Registry

http://dire.dcode.org

Web server based on the Enhancer Identification (EI) method, to determine the chromosomal location and functional characteristics of distant regulatory elements (REs) in higher eukaryotic genomes. The server uses gene co-expression data, comparative genomics, and combinatorics of transcription factor binding sites (TFBSs) to find TFBS-association signatures that can be used for discriminating specific regulatory functions. DiRE's unique feature is the detection of REs outside of proximal promoter regions, as it takes advantage of the full gene locus to conduct the search. DiRE can predict common REs for any set of input genes for which the user has prior knowledge of co-expression, co-function, or other biologically meaningful grouping. The server predicts function-specific REs consisting of clusters of specifically-associated TFBSs, and it also scores the association of individual TFs with the biological function shared by the group of input genes. Its integration with the Array2BIO server allows users to start their analysis with raw microarray expression data.

Proper citation: Distant Regulatory Elements (RRID:SCR_003058) Copy   

•   Source: SciCrunch Registry

http://www.scienceexchange.com/facilities/hybridoma-center-wustl

The Hybridoma Center / Monoclonal Antibody Development Core is a specialized cell culture facility that assists investigators in the generation of monoclonal antibody producing B cell hybridomas. Mouse and Armenian hamster models are utilized to generate antigen reactive monoclonal antibodies.

Proper citation: WUSTL Hybridoma Center (RRID:SCR_012226) Copy   

•   Source: SciCrunch Registry

http://www.scienceexchange.com/facilities/anti-infectives-screening-and-insectary-core-facilities-nyu

Our insectary produces five rodent malaria strains weekly and will ship live sporozoite infected Anopheles stephensi to investigators for research use (Plasmodium berghei GFP, luciferase or red-star and P. yoelii-GFP) Anti-infective testing including in vitro EC50, in vivo mice infection are available against for major parasitic diseases: Malaria, Leishmaniasis, Chagas and African Trypanosomiasis.

Proper citation: NYU Anti-Infectives Screening and Insectary Core Facilities (RRID:SCR_012350) Copy   

•   Source: SciCrunch Registry

http://www.scienceexchange.com/facilities/gene-targeting-and-transgenic-core-rochester

Currently, the Gene Targeting and Transgenic Core''s services include the production of mouse models using DNA microinjection and embryonic stem cell injection (from gene targeting in mouse ES cells to production of chimeric mice) methodologies. Additional services have included: various analytical techniques, embryo cryopreservation, rederivation of pathogen-free rodents, and assisted reproduction techniques (e.g., in vitro fertilization (IVF), superovulation, and embryo transfer). Specific strains, and alternative species and methods are considered when appropriate for individual research applications.

Proper citation: URMC Gene Targeting and Transgenic Core (RRID:SCR_012367) Copy   

•   Source: SciCrunch Registry

http://www.openbioinformatics.org/annovar/

An efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, as well as mouse, worm, fly, yeast and many others). Given a list of variants with chromosome, start position, end position, reference nucleotide and observed nucleotides, ANNOVAR can perform: 1. gene-based annotation. 2. region-based annotation. 3. filter-based annotation. 4. other functionalities. (entry from Genetic Analysis Software)

Proper citation: ANNOVAR (RRID:SCR_012821) Copy   

•   Source: SciCrunch Registry

http://www.sbpdiscovery.org/technology/sr/Pages/LaJolla_TumorAnalysis.aspx

Facility that provides analysis of animal models of human cancer and other diseases. It provides investigators access to a wide variety of human cancer cell lines for xenograft studies, some primary human xenograft models and additional transgenic mouse solid tumors and leukemia models. The core also offers serial passaging of tumors and derivation of 2D and 3D cultures from xenograft tumors, including patient-derived xenograft (PDX) models. These short-term cell cultures established from PDXs enable in vitro analysis including high throughput screening with compounds or RNAi for functional characterization.

Proper citation: Sanford Burnham Prebys Medical Discovery Institute Tumor Analysis (RRID:SCR_014858) Copy   

•   Source: SciCrunch Registry

http://www.chibi.ubc.ca/Gemma

Resource for reuse, sharing and meta-analysis of expression profiling data. Database and set of tools for meta analysis, reuse and sharing of genomics data. Targeted at analysis of gene expression profiles. Users can search, access and visualize coexpression and differential expression results.

Proper citation: Gemma (RRID:SCR_008007) Copy   

•   Source: SciCrunch Registry

http://bmbpcu36.leeds.ac.uk/RE1db_mkII/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 15, 2013. A database containing all genomic human and mouse binding sites of the Repressor Element 1 Silencing Transcription factor (REST), identified by PSSM. The RE1 silencing transcription factor (REST; also known as the neuron-restrictive silencer factor), is a nine zinc-finger transcription factor, related to the Gli-Kruppel family. REST binds to a conserved 21-nucleotide element, known as repressor element 1 (RE1; also known as the neuron-restrictive silencer element). REST was proposed to be a ''master'' silencer of neuron specific gene expression in non-neuronal tissues and undifferentiated neuroepithelium (precursor of neuronal cells), preventing the default expression of the neuronal phenotype during embryogenesis. It has been shown to function independently of orientation and distance from a gene promoter. REST has an important role during embryonic development, as homozygous gene knockout mice (Rest-/-) die by embryonic day 11.5. The constitutive expression of REST has also been shown to disrupt neuronal gene expression and cause axon path finding errors in chicken embryos (Paquette et al. 2000). RE1 sequences that are known to bind REST have also been found near to non-neuronal genes, including keratin and cytochrome P450 genes.

Proper citation: Neuron-Restrictive Silencer Factor (RRID:SCR_008546) Copy   

•   Source: SciCrunch Registry

http://www.brainnav.com

THIS RESOURCE IS NO LONGER IN SERVICE, documented December 31, 2013. An interactive atlas and 3D brain software for research, structure analysis, and education, it offers six atlases representing four species: the mouse, rat, monkey and human. The stereotaxic coordinates atlases are available for all four species and the rodent models have additional chemoarchitectonic atlases. BrainNavigator helps locate specific areas of the brain, making visualizing and experimental planning in the brain easier. *Plan: Browse 6 Atlases, Visualize with 3D models, Search Literature, Analyze gene expression, Identify connections *Publish: Access reference tools, Use and print images for publication, Search literature *Propose: Use and print images for proposals, Search literature, Locate gene expression in 2D and 3D, Identify connections *Produce: Simulate injections, Customize new coordinates, virtually slice sections, overlay atlas maps on your own images, create personal atlas maps With BrainNavigator, you''ll gain 24/7 access to their powerful 3D brain interactive software tool that helps further research in the neurosciences. In addition, their vast library of widely respected and referenced brain publications will provide a plethora of information on the most current brain research available. As publisher of the gold standard in brain atlas publications authored by the team around the leading brain cartographers George Paxinos and Charles Watson, they are pleased to bring an advanced tool to today''s neuroscientists and educators. Combining atlas content and 3D capabilities based on technologies from the Allen Institute for Brain Science, this online workflow solution brings brain research, analysis and education tools to your fingertips.

Proper citation: BrainNavigator (RRID:SCR_008289) Copy   

•   Source: SciCrunch Registry

http://www.stanford.edu/group/exonarray/cgi-bin/plot_selector.pl

Transcriptome database of acutely isolated purified astrocytes, neurons, and oligodendrocytes. Provides improved cell-type-specific markers for better understanding of neural development, function, and disease.

Proper citation: Exon Array Browser (RRID:SCR_008712) Copy   

•   Source: SciCrunch Registry

http://dnatraffic.ibb.waw.pl/

DNAtraffic database is dedicated to be an unique comprehensive and richly annotated database of genome dynamics during the cell life. DNAtraffic contains extensive data on the nomenclature, ontology, structure and function of proteins related to control of the DNA integrity mechanisms such as chromatin remodeling, DNA repair and damage response pathways from eight model organisms commonly used in the DNA-related study: Homo sapiens, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Escherichia coli and Arabidopsis thaliana. DNAtraffic contains comprehensive information on diseases related to the assembled human proteins. Database is richly annotated in the systemic information on the nomenclature, chemistry and structure of the DNA damage and drugs targeting nucleic acids and/or proteins involved in the maintenance of genome stability. One of the DNAtraffic database aim is to create the first platform of the combinatorial complexity of DNA metabolism pathway analysis. Database includes illustrations of pathway, damage, protein and drug. Since DNAtraffic is designed to cover a broad spectrum of scientific disciplines it has to be extensively linked to numerous external data sources. Database represents the result of the manual annotation work aimed at making the DNAtraffic database much more useful for a wide range of systems biology applications. DNAtraffic database is freely available and can be queried by the name of DNA network process, DNA damage, protein, disease, and drug.

Proper citation: DNAtraffic (RRID:SCR_008886) Copy   

•   Source: SciCrunch Registry

https://scicrunch.org/scicrunch/data/source/nlx_154697-3/search?q=*

A virtual database currently indexing available cell lines from: Coriell Cell Repositories, International Mouse Strain Resource (IMSR), ATCC, NIH Human Pluripotent Stem Cell Registry, NIGMS Human Genetic Cell Repository, and Developmental Therapeutics Program.

Proper citation: Integrated Cell Lines (RRID:SCR_008994) Copy   

•   Source: SciCrunch Registry

http://connectivity.brain-map.org/

Map of neural connections in mouse brain, built on an array of transgenic mice genetically engineered to target specific cell types. In addition to the connectivity data, information about the transgenic mouse lines and genetic tracers is available. Consists of high resolution 2-D projectivity image data that can be viewed side-by-side with the associated reference atlas and other reference datasets. Enables 3-D visualization and spatial/ontological search of connectivity models through a combination of manual and informatics analyses.

Proper citation: Allen Mouse Brain Connectivity Atlas (RRID:SCR_008848) Copy   

•   Source: SciCrunch Registry

http://www.benoslab.pitt.edu/comir/

Data analysis service that predicts whether a given mRNA is targeted by a set of miRNAs. ComiR uses miRNA expression to improve and combine multiple miRNA targets for each of the four prediction algorithms: miRanda, PITA, TargetScan and mirSVR. The composite scores of the four algorithms are then combined using a support vector machine trained on Drosophila Ago1 IP data.

Proper citation: ComiR (RRID:SCR_013023) Copy   

•   Source: SciCrunch Registry

http://gsgator.ewha.ac.kr/

A web-based platform for functional interpretation of gene sets with features such as cross-species Gene Set Analysis (GSA), Flexible and Interactive GSA, simultaneous GSA for multiple gene set, and and a fully integrated network viewer for both visualizing GSA results and molecular networks.

Proper citation: gsGator (RRID:SCR_012035) Copy   

•   Source: SciCrunch Registry

http://www.scienceexchange.com/facilities/transgenic-mouse-shared-resource-columbia

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 22, 2024. Core facility that specializes in the generation and analysis of genetically modified mice, including transgenic and knockout animals, is an essential technology for biomedical research. Our services include: Production of transgenic mice by pronuclear DNA microinjection and embryo transfer. Production of chimeric mice by blastocyst injection of genetically modified ES cells and embryo transfer, which is part of the procedure of producing knockout or knockin mice. Gene targeting, which involves the electroporation of a targeting vector into pluripotent mouse embryonic stem (ES) cells and the selection of gene-targeted clones. Education of investigators and advice on vector and experimental design for experiments using transgenic and knockout mice. Bioimaging: The Animal Imaging Service provides investigators the opportunity for non-invasive detection, localization, and longitudinal monitoring of primary and metastatic cancer cells in vivo, in allograft, zenograft, transgenic and knock-out mouse models. The IVIS Spectrum (Caliper Life Sciences, Hopkinton MA) uses optical imaging technology to detect bioluminescent and fluorescent reporters across the blue to near infrared wavelength region. DNA samples and ES cell lines are injected in the order in which the signed service request forms are received. Currently, the average time from receipt of the service request to injection is approximately 2 weeks. For ES Cell electroporation and expansion, success in gene targeting cannot be guaranteed due to inherent variability in the frequency of targeting different loci, and the possibility of mistakes or mutations in the targeting vector.

Proper citation: Columbia Transgenic Mouse Shared Resource (RRID:SCR_012640) 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://www.informatics.jax.org/external/festing/mouse/STRAINS.shtml

A list of major inbred mouse strains from the Jackson laboratories. This list is not being actively maintained (found on Nov 27, 2013).

Proper citation: MGI strains (RRID:SCR_012950) Copy   

•   Source: SciCrunch Registry