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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://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://mouse.brain-map.org/static/brainexplorer

Atlas of the brain and the disorders affecting it, aimed at general practitioners and specialists in training. It consists of three main parts: a description of the different parts of the normal brain and their functions, a description of the process of neurological control, and a description of 14 different brain disorders in psychiatry and neurology - as well as their cause, symptoms, and treatment.

Proper citation: Brain Explorer Atlas and Teaching Tool (RRID:SCR_013022) Copy   

•   Source: SciCrunch Registry

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

For each developmental stage (using the staging system defined by Theiler), the Mouse Anatomical Dictionary organizes the terms hierarchically from body region or system to tissue to tissue substructure. Modeling the anatomy hierarchically makes it possible to record expression results from assays with differing spatial resolution in a consistent and integrated manner. The Mouse Anatomical Dictionary Browser lets you navigate the extensive dictionary hierarchies for the different developmental stages, locate specific anatomical structures within those hierarchies, and see the expression results associated with those structures. Stages 1 through 26 (embryonic development) are being developed at the Department of Biomedical Sciences, University of Edinburgh, Scotland and the MRC Human Genetics Unit, Edinburgh, as part of The Mouse Atlas and 3D Graphical Gene Expression Database Project. Stage 28 (postnatal mouse) is being developed by the Gene Expression Database Project at The Jackson Laboratory.

Proper citation: Mouse Anatomical Dictionary Browser (RRID:SCR_012778) Copy   

•   Source: SciCrunch Registry

http://cleversysinc.com/?csi_products=homecagescan

Software used for automatic high throughput analysis of unconstrained rodent behaviors in a home cage. HomeCageScan is ideal for longitudinal studies where several animals are studied and tested over long periods. Its features include twenty-four-hour recording capabilities, statistical analysis, automatic adaptation to environmental changes (including day and night changes), and a batch‐mode which allows user to run multiple videos successively without human intervention. The software can detect various behaviors ranging from feeding and urination to jumping and foraging.

Proper citation: HomeCageScan (RRID:SCR_014253) Copy   

•   Source: SciCrunch Registry

http://actimetrics.com/products/clocklab/

Point and click program used to quickly analyse circadian activity data using algorithms and embedded controls to make every graph interactive and useful for data analysis. The analysis program has been used for a variety of species including mice, hamsters, rats, sheep, Drosophila, and humans. This program has three separate applications: one for data collection, one for analysis, and a chamber control program.

Proper citation: Clocklab (RRID:SCR_014309) Copy   

•   Source: SciCrunch Registry

http://marrvel.org/

Web tool to search multiple public variant databases simultaneously and provide a unified interface to facilitate the search process. Used for integration of human and model organism genetic resources to facilitate functional annotation of the human genome. Used for analysis of human genes and variants by cross-disciplinary integration of records available in public databases to facilitate clinical diagnosis and basic research.

Proper citation: MARRVEL (RRID:SCR_016871) Copy   

•   Source: SciCrunch Registry

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

Portal provides access to data and web based applications created for benefit of global research community by Allen Institute for Brain Science. Projects to ombine genomics with neuroanatomy by creating gene expression maps for mouse and human brain. Mouse Brain Atlas, Human Brain Atlas, Developing Mouse Brain Atlas, Developing Human Brain Atlas, Mouse Connectivity Atlas, Non-Human Primate Atlas, and Mouse Spinal Cord Atlas and three related projects Glioblastoma, Mouse Diversity, and Sleep data banks, are used to advance various fields of science especially in neurobiological diseases.

Proper citation: Allen Brain Atlas (RRID:SCR_017001) Copy   

•   Source: SciCrunch Registry

http://www.bx.psu.edu/~giardine/vision/

International project to analyze mouse and human hematopoiesis, and provide a tractable system with clear clinical significance and importance to NIDDK. Collection of information from the flood of epigenomic data on hematopoietic cells as catalogs of validated regulatory modules, quantitative models for gene regulation, and a guide for translation of research insights from mouse to human.

Proper citation: ValIdated Systematic IntegratiON of epigenomic data (RRID:SCR_016921) Copy   

•   Source: SciCrunch Registry

https://github.com/Sethupathy-Lab/miRquant

Software tool for accurate annotation and quantification of microRNAs and their isomiRs from small RNA-sequencing data. Provides information on quality of sequencing data, genome mapping statistics, abundance of other types of small RNAs such as tDRs and yDRs, prevalence of post transcriptional modifications.

Proper citation: miRquant (RRID:SCR_017261) Copy   

•   Source: SciCrunch Registry

https://nyumc.ilab.agilent.com/service_center/4273

Core offers services for researchers who want to apply advanced molecular genetic techniques in rodent models of physiology and disease. Provides expertise in generating novel mutant and transgenic mouse strains using genome engineering in mouse embryos and in embryonic stem cells (ESCs). Available technologies include:Generation of genome-edited mice by embryo pronuclear microinjection of DNA and genome editors (e.g., CRISPR/Cas9, site-specific recombinases) or traditional BAC transgenesis;Generation of genome-edited mice from mouse embryonic stem cells (mESCs) by chimeric blastocyst injection;Generation of genome-edited mice from mESCs by tetraploid blastocyst injection; Generation of mice from induced pluripotent stem cells;Assisted reproductive technologies; Sperm and embryo cryopreservation, storage and import/export;in vitro fertilization (IVF); Embryo rederivation technologies for animal import into barrier vivaria through quarantine.

Proper citation: NYU Langone’s Advanced Rodent Transgenics Laboratory ART-Lab Core Facility (RRID:SCR_017692) Copy   

•   Source: SciCrunch Registry

http://159.149.160.51/cscan/

Data resource that includes a large collection of genome-wide ChIP-Seq experiments performed on transcription factors (TFs), histone modifications, RNA polymerases and others. Enriched peak regions from the ChIP-Seq experiments are crossed with the genomic coordinates of a set of input genes, to identify which of the experiments present a statistically significant number of peaks within the input genes' loci. The input can be a cluster of co-expressed genes, or any other set of genes sharing a common regulatory profile. Users can thus single out which TFs are likely to be common regulators of the genes, and their respective correlations. Also, by examining results on promoter activation, transcription, histone modifications, polymerase binding and so on, users can investigate the effect of the TFs (activation or repression of transcription) as well as of the cell or tissue specificity of the genes' regulation and expression.

Proper citation: Cscan (RRID:SCR_006756) Copy   

•   Source: SciCrunch Registry

http://cellfinder.de/

Database of mapped validated gene and protein expression, phenotype and images related to cell types. The data allow characterization and comparison of cell types and can be browsed by using the body browser and by searching for cells or genes. All cells are related to more complex systems such as tissues, organs and organisms and arranged according to their position in development. CellFinder provides long-term data storage for validated and curated primary research data and provides additional expert-validation through relevant information extracted from text. Operated under the Open Source/Access model, community and scientific networking applications will allow users to store and retrieve their data and to explore cells and their interactions on singular and complex resolution levels. The involvement of stem cell registries and banks will allow direct access to selected cells. The set up the stem cell data repository will involve three lines of action: * the acquisition of scientific data and contents * the standardized description of this data, its organization with the help of ontologies and technical implementation * the integration of existing sources/logistics and to ensure sustainable long-term operation

Proper citation: CellFinder (RRID:SCR_006598) Copy   

•   Source: SciCrunch Registry

http://bar.utoronto.ca/welcome.htm

Web-based tools for working with functional genomics and other data, including Gene Expression and Protein Tools, Molecular Markers and Mapping Tools, and Other Genomic Tools. Most are designed with the plant (mainly Arabidopsis) researcher in mind, but a couple of them can be useful to the wider research community, e.g. Mouse eFP Browser or BlastDigester. The associated paper for most tools is available.

Proper citation: BAR (RRID:SCR_006748) Copy   

•   Source: SciCrunch Registry

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

Ontology that organizes anatomical structures for the adult mouse (Theiler stage 28) spatially and functionally, using ''is a'' and ''part of'' relationships. The ontology is used to describe expression data for the adult mouse and phenotype data pertinent to anatomy in standardized ways. The browser can be used to view anatomical terms and their relationships in a hierarchical display.

Proper citation: Adult Mouse Anatomy Ontology (RRID:SCR_006568) Copy   

•   Source: SciCrunch Registry

https://madb.nci.nih.gov/

Microarray data management and analysis system for NCI / Center for Cancer Research scientists / collaborators. Data is secured and backed up on a regular basis, and investigators can authorize levels of access privileges to their projects, allowing data privacy while still enabling data sharing with collaborators.

Proper citation: mAdb (RRID:SCR_006677) Copy   

•   Source: SciCrunch Registry

http://idm.fudan.edu.cn/PBmice/

Database for storing, retrieving, and displaying the information derived from piggyBac (PB) insertions (Insert) and their characterizations in the mouse genome with piggyBac transposon system. Quick Search and Advanced Search tools have been provided to find information in the PBmice database, the result is centered on Inserts and provides information related to the Inserts. A mapping database is linked to PBmice too. This mapping database allows row experiment data to be inputted in. All the mature data can be allowed publish to PBmice. PBmice Source Code is available with a License Agreement.

Proper citation: PBmice (RRID:SCR_006978) Copy   

•   Source: SciCrunch Registry

http://brainmaps.org

An interactive multiresolution brain atlas that is based on over 20 million megapixels of sub-micron resolution, annotated, scanned images of serial sections of both primate and non-primate brains and integrated with a high-speed database for querying and retrieving data about brain structure and function. Currently featured are complete brain atlas datasets for various species, including Macaca mulatta, Chlorocebus aethiops, Felis catus, Mus musculus, Rattus norvegicus, Tyto alba and many other vertebrates. BrainMaps is currently accepting histochemical, immunocytochemical, and tracer connectivity data, preferably whole-brain. In addition, they are interested in EM, MRI, and DTI data.

Proper citation: BrainMaps.org (RRID:SCR_006878) Copy   

•   Source: SciCrunch Registry