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http://bioit.fleming.gr/fleming/

A database of all mouse strains developed and/or housed in the Alexander Fleming Biomedical Sciences Research Center (BSRC), Greece, available to both internal and external researchers. The animal house unit provides its services to the various research groups of the BSCR as well as to external contractors in Europe and U.S.A. (pharmaceutical and biotechnology companies, leading hospitals, and academic institutions). The information provided includes: general information (i.e. internal Fleming contact, original mouse creator, allelic composition and MTA details), availability (i.e. available genetic background and strain state), allele & mutations (i.e. allele name and symbol and mutation type), publications and handling & genotyping instructions.

Proper citation: Fleming Database (RRID:SCR_008920) Copy   

•   Source: SciCrunch Registry

https://alleninstitute.org/

Non profit bioscience research organization in Seattle, Washington dedicated to accelerating research globally and sharing that data within the science community. Allen Institute for Brain Science, Allen Institute for Cell Science, Allen Institute for Immunology, and The Paul G. Allen Frontiers Group are four divisions of this Institute with commitment to open science model within its research institutes.

Proper citation: Allen Institute (RRID:SCR_005435) Copy   

•   Source: SciCrunch Registry

https://www.jax.org/jax-mice-and-services/in-vivo-pharmacology/neurobiology-services

A laboratory that researches neurological diseases, including amyotrophic lateral sclerosis, Alzheimer's disease, glaucoma, retinitis pigmentosa, epilepsy, and hearing disorders. The Laboratory offers courses that train and update neuroscience researchers. It distributes JAX Mice models suitable for neuroscience research. Also available are research tools for neurobiology.

Proper citation: Jackson Laboratory Neurobiology (RRID:SCR_005570) Copy   

•   Source: SciCrunch Registry

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

Repository of Cre Driver lines and related information resources. Their services include analysis of Cre line excision function in both target and non-target tissues using Cre reporter lines and presenting the annotated data in the expression data portion of this website, http://cre.jax.org/data.html.

Proper citation: JAX Cre Repository (RRID:SCR_005566) Copy   

•   Source: SciCrunch Registry

http://pivotcollections.org/collection.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 4th, 2023. Mouse brains displayed in the Microsoft Silverlight PivotViewer from the Mouse Brain Library (MBL) which consist of high-resolution images of brains from many genetically characterized strains of mice. PivotViewer makes it easier to interact with massive amounts of data on the web in ways that are powerful, informative, and fun. By visualizing thousands of related items at once, users can see trends and patterns that would be hidden when looking at one item at a time. Because PivotViewer leverages Deep Zoom, it displays full, high-resolution content without long load times, while the animations and natural transitions provide context and prevent users from feeling overwhelmed by large quantities of information. This simple, inviting interaction model encourages exploration and longer audience engagement times, and applies broadly to a variety of content types.

Proper citation: MBL Pivot Collection (RRID:SCR_005506) Copy   

•   Source: SciCrunch Registry

http://cgap.nci.nih.gov/Genes/GOBrowser

With the CGAP GO browser, you can browse through the GO vocabularies, and find human and mouse genes assigned to each term. GO data updated every few months. Platform: Online tool

Proper citation: CGAP GO Browser (RRID:SCR_005676) Copy   

•   Source: SciCrunch Registry

http://genenet2.uthsc.edu/geneinfoviz/search.php

GeneInfoViz is a web based tool for batch retrieval of gene function information, visualization of GO structure and construction of gene relation networks. It takes a input list of genes in the form of LocusLink ID, UniGeneID, gene symbol, or accession number and returns their functional genomic information. Based on the GO annotations of the given genes, GeneInfoViz allows users to visualize these genes in the DAG structure of GO, and construct a gene relation network at a selected level of the DAG. Platform: Online tool

Proper citation: GeneInfoViz (RRID:SCR_005680) Copy   

•   Source: SciCrunch Registry

http://celltypes.org/

Central repository of information on neuronal cell types mainly accumulating information on: Genetically labeled cell types in mouse brain and genetically engineered mouse lines for cell type research. Mouse lines are annotated with * Atlas for examining transgene expression patterns * Information on construct used to generate transgene * Associated publications * Anatomical regions where transgene is expressed (based on Atlas) * Information on where to obtain the animals Currently, the mouse lines in the database are mostly generated at Cold Spring Harbor Lab, Scripps Research Institute, Baylor College of Medicine and Brandeis University with few other exceptions. In the future, they will incorporate more mouse lines useful for neuronal cell type research. Cell types are annotated with * Anatomical region * Properties (frequently used terms in neuroscience research) * Mouse line used to define the cell type * Genome wide transcriptome data (if available) * Specific (marker) genes (if available) * Marker immunostaining data (if available) * Associated publications * Electrophysiological characterizations (when available) * Morphological characterizations (when available)

Proper citation: celltypes.org (RRID:SCR_004545) Copy   

•   Source: SciCrunch Registry

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

Community ontology to provide standard terms for annotating mammalian phenotypic data. It has a hierarchical structure that permits a range of detail from high-level, broadly descriptive terms to very low-level, highly specific terms. This range is useful for annotating phenotypic data to the level of detail known and for searching for this information using either broad or specific terms as search criteria. Your input is welcome.

Proper citation: MPO (RRID:SCR_004855) Copy   

•   Source: SciCrunch Registry

http://jaxmice.jax.org/strain/007910.html

These Brainbow 1.0 (founder line L) mice allow labeling of individual neuronal types (specifically hippocampal neuron cell bodies, and including motor neurons, dentate gyrus granule cells, pyramidal neurons of the cortex and CA1 area) with approximately 166 distinguishable color variations in cre recombined cells, and may also be useful in conjunction with other Brainbow strains (Stock No. 007901, Stock No. 007911, Stock No. 007921) for neurobiological studies. These Thy1-Brainbow 1.0 (line L) transgenic mice are viable and fertile. The mice possess multiple fluorescent protein sequences uniquely flanked with pairs of incompatible Lox sites alternated to create mutually exclusive recombination events; allowing stochastic expression of multiple fluorescent proteins from a single transgene. Prior to Cre-mediated recombination, the fluorescent protein immediately adjacent to the promoter, dTomato (RFP), is expressed in peripheral and central neurons. When bred to Cre recombinase expressing mice, the resulting offspring can have one of three expression outcomes for each transgene in each cell of the cre expressing tissue(s): dTomato (RFP) (no recombination), mCerulean (CFP), or mYFP. Integration of tandem transgene copies yields combinatorial fluorescent protein expression in each cell, and thus many possible cell colors, providing a way to distinguish adjacent neurons and visualize other cellular interactions. Of note, the single FRT site inserted in the transgene allows tandem transgene copy number reduction through Flp-mediated recombination if desired. These Brainbow 1.0 (founder line L) mice were found to have multiple transgene copies that allow labeling of individual neuronal types (specifically hippocampal neuron cell bodies, and including motor neurons, dentate gyrus granule cells, pyramidal neurons of the cortex and CA1 area) with approximately 166 distinguishable color variations in cre recombined cells, and may also be useful in conjunction with other Brainbow strains (Stock No. 007901, Stock No. 007911, Stock No. 007921) for neurobiological studies. This mouse can be used to support research in many areas including:
Neurobiology Research
* Cre-lox System (loxP-flanked Sequences)
* Fluorescent protein expression in neural tissue
Research Tools
* Cre-lox-System (loxP-flanked Sequences: Test/Reporter)
* Developmental Biology Research (Cre-lox system)
* Developmental Biology Research (transplantation marker for embryonic and adult tissue)
* FLP-FRT System (FRT-flanked Sequences)
* Fluorescent Proteins * Genetics Research (Mutagenesis and Transgenesis: Cre-lox system) * Genetics Research (Tissue/Cell Markers: Cre-lox system) * Genetics Research (Tissue/Cell Markers: astrocyte-specific marker) * Genetics Research (Tissue/Cell Markers: astrocytes) * Genetics Research (Tissue/Cell Markers: astrocytes, neurons) * Genetics Research (Tissue/Cell Markers: glial cells) * Genetics Research (Tissue/Cell Markers: multiple) * Genetics Research (Tissue/Cell Markers: neurons) * Genetics Research (Tissue/Cell Markers: transplantation marker for embryonic and adult tissue) * Neurobiology Research (astrocyte-specific marker) * Neurobiology Research (cell marker) * YFP related Research Tools * Fluorescent Proteins Control: 000664 C57BL/6J (approximate)

Proper citation: Brainbow mouse resource at Jackson Labs (RRID:SCR_004894) Copy   

•   Source: SciCrunch Registry

https://datashare.ed.ac.uk/handle/10283/3844

Genome transcriptome atlas by RNA in situ hybridization on sagittal sections of developing mouse at embryonic day 14.5. Consists of searchable database of annotated images that can be interactively viewed. Anatomy based expression profiles for coding genes and microRNAs, tissue specific genes. Expression data generated by using human and murine tissue arrays.

Proper citation: Eurexpress (RRID:SCR_005093) Copy   

•   Source: SciCrunch Registry

http://cbil.upenn.edu/BEERS/

A simulation engine for generating RNA-Seq data that was designed to benchmark RNA-Seq alignment algorithms and also algorithms that aim to reconstruct different isoforms and alternate splicing from RNA-Seq data. By default BEERS simulates either mouse or human paired-end RNA-Seq data modeled on the illumina platform. It starts with a large number of gene models (approx 500K) taken from about ten different published annotation efforts, and then chooses a fixed number of these genes at random (30,000 by default). This avoids biasing for or against any particular set of annotations. BEERS then introduces substitutions, indels, alternate spice forms, sequencing errors, and intron signal. BEERS can also simulate strand specific reads. BEERS does not simulate quality scores. There are four configuration files required, these are available for human and mouse. BEERS can also be configured to use any set of gene models. Pre-built indexes for human refseq are given. Using these indexes will generate a much tamer set of transcripts. BEERS is written in perl.

Proper citation: BEERS (RRID:SCR_005090) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/PHENOMEBLAST

A cross-species phenotype and anatomy ontology resulting from combining available anatomy and phenotype ontologies and their definitions. The ontology includes phenotype definitions for yeast, mouse, fish, worm, fly and human phenotypes and diseases.

Proper citation: PhenomeBLAST Ontology (RRID:SCR_005139) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/ABA-AMB

Allen Brain Atlas P56 Mouse Ontology

Proper citation: ABA Adult Mouse Brain Ontology (RRID:SCR_010286) Copy   

•   Source: SciCrunch Registry

http://mirdb.org/miRDB/

An online database for miRNA target prediction and functional annotations.

Proper citation: miRDB (RRID:SCR_010848) Copy   

•   Source: SciCrunch Registry

http://targetscan.org/

Web tool to predict biological targets of miRNAs by searching for presence of conserved 8mer, 7mer and 6mer sites that match seed region of each miRNA. Nonconserved sites are also predicted and sites with mismatches in seed region that are compensated by conserved 3' pairing. Used to search for predicted microRNA targets in mammals.

Proper citation: TargetScan (RRID:SCR_010845) Copy   

•   Source: SciCrunch Registry

http://archive.igbmc.fr/recherche/Prog_FGC/Eq_HGron/Polyphemus.html

R package for comparative analysis of RNA Polymerase II ChIP-Seq profiles by non-linear normalization.

Proper citation: POLYPHEMUS (RRID:SCR_010870) Copy   

•   Source: SciCrunch Registry

http://adacgh.bioinfo.cnio.es/

A web tool for the analysis of aCGH data sets. They focus on calling gains and losses and estimating the number of copy changes. Note: ADaCGH will continue being maintained, but is deprecated. Their new tool for CGH and CNV is WaviCGH, http://wavi.bioinfo.cnio.es/

Proper citation: ADaCGH (RRID:SCR_010916) Copy   

•   Source: SciCrunch Registry

http://www.zi-mannheim.de/en.html

An independent public foundation of the State of Baden-Wuerttemberg associated with the University of Heidelberg, that is one of Europe''s premier research institutions dedicated to mental health. The CIMH combines a clinical inpatient (300 beds) and outpatient program in adult psychiatry, addiction, childhood and adolescent psychiatry and psychotherapy with outstanding research facilities, including two dedicated research fMRI scanners (currently 1.5 Ts and 3 Ts, from next summer 2 3 Ts magnets), an 9.4 Ts animal fMRI scanner, high-throughput facilities for genotyping and molecular biology, neuropsychology and an extensive transgenic animal (both mice and rats) and animal behavior assessment facility.

Proper citation: Central Institute of Mental Health; Mannheim; Germany (RRID:SCR_011144) Copy   

•   Source: SciCrunch Registry

http://www.scienceexchange.com/facilities/precision-targeting-lab-ptl-llc

THIS RESOURCE IS NO LONGER IN SERVICE, documented on February 3rd, 2022. Provides mouse genetic services. PTL develops proprietary technologies for the production of transgenic and genetically modified mice. One of PTL''s key technologies increases gene targeting frequency from 0%-5% to 30%-60% in mouse ES cells. Improvement in gene targeting frequency speeds up the production process of genetically modified mouse models. This translates into less production cost and faster delivery of our products. Genetically modified mouse models are guaranteed for delivery within 12 months or less with PTL''s full gene targeting services.

Proper citation: Precision Targeting Lab LLC (RRID:SCR_011013) Copy   

•   Source: SciCrunch Registry