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http://ccr.coriell.org/Sections/Collections/CSCB/Default.aspx

Biospecimen repository that provides scientists with the opportunity to bank their pluripotent stem cell lines and develops in-house induced pluripotent stem cell (iPSC) lines for distribution. They have developed core capabilities to maintain, characterize, bank, and distribute important stem cell resources. The SCB performs extensive identification and characterization testing for all submitted human induced pluripotent stem cell (iPSC) and mouse embryonic stem cell (mES) lines. The identification and quality control measures include karyotype analysis, microsatellite analysis for parental cell line identity matching, sterility testing, and assessment of viability after cryopreservation. Pluripotency characterizations performed by SCB vary depending upon the distributing repository. * NIGMS iPSCs: Surface antigen expression, Embryoid body formation, Pluritest Gene Expression assay * NINDS iPSCs: Surface antigen expression, Embryoid body formation * NIA mES: Surface antigen expression, Embryoid body formation, Transgene induction Each characterized human iPSC line and mES line released for distribution is provided with a Certificate of Analysis, which includes information regarding characterization and quality of the line, images and links to original publications. The human iPSCs distributed by Coriell are strictly for research purposes and cannot be used in human subjects. All terms described in the Material Transfer Agreement (NIGMS and NINDS Repositories) or Assurance Form (NIA Repository) for the stem cell line must be agreed to prior to using stem cell lines from Coriell.

Proper citation: Coriell Institute Stem Cell Biobank (RRID:SCR_008745) Copy   

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https://www.janelia.org/confocal-imagery-management-and-analysis-tools

A discovery platform used to analyze and annotate imagery for individual projects, while assembling shared data resources. It was originally applied to Drosophila neuronal anatomy and neuroblast lineage analysis and is currently being extended to support mouse whole-brain projection tracing. The Workstation is both a pipeline management system that extracts entities from 3D imagery and a suite of tools that enable scientists to annotate large imagery datasets. A Entity-Attribute-Value (EAV) graph permits any element to be annotated by users with custom ontologies. By allowing any entity to have multiple parents, the graph can be re-arranged by each user without copying the underlying image data.

Proper citation: Janelia Workstation (RRID:SCR_014302) Copy   

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http://www.gensat.org/daily_showcase.jsp

THIS RESOURCE IS NO LONGER IN SERVICE, documented on March 19, 2012. Due to budgetary constraints, the National Center for Biotechnology Information (NCBI) has discontinued support for the NCBI GENSAT database, and it has been removed from the Entrez System. The Gene Expression Nervous System Atlas (GENSAT) project involves the large-scale creation of transgenic mouse lines expressing green fluorescent protein (GFP) reporter or Cre recombinase under control of the BAC promoter in specific neural and glial cell populations. BAC expression data for all the lines generated (over 1300 lines) are available in online, searchable databases (www.gensat.org and the Database of GENSAT BAC-Cre driver lines). If you have any specific questions, please feel free to contact us at info_at_ncbi.nlm.nih.gov The GENSAT project aims to map the expression of genes in the central nervous system of the mouse, using both in situ hybridization and transgenic mouse techniques. Search criteria include gene names, gene symbols, gene aliases and synonyms, mouse ages, and imaging protocols. Mouse ages are restricted to E10.5 (embryonic day 10.5), E15.5 (embryonic day 15.5), P7 (postnatal day 7), and Adult (adult). The project focuses on two techniques * Evaluation of unmodified mice lines for expression of a given gene using radiolabelled riboprobes and in-situ hybridization. * Creation of transgenic mice lines containing a BAC construct that expresses a marker gene in the same environment as the native gene

Proper citation: GENSAT at NCBI - Gene Expression Nervous System Atlas (RRID:SCR_003923) Copy   

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http://www.inmex.ca./INMEX/

A web-based tool to support meta-analysis of multiple gene-expression data sets, as well as to enable integration of data sets from gene expression and metabolomics experiments. INMEX contains three functional modules. The data preparation module supports flexible data processing, annotation and visualization of individual data sets. The statistical analysis module allows researchers to combine multiple data sets based on P-values, effect sizes, rank orders and other features. The significant genes can be examined in functional analysis module for enriched Gene Ontology terms or Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, or expression profile visualization. INMEX has built-in support for common gene/metabolite identifiers (IDs), as well as 45 popular microarray platforms for human, mouse and rat. Complex operations are performed through a user-friendly web interface in a step-by-step manner.

Proper citation: INMEX (RRID:SCR_004173) Copy   

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https://scicrunch.org/scicrunch/data/source/nlx_154697-4/search?q=*

Virtual database indexing brain region gene expression data from mice from: Gene Expression Nervous System Atlas (GENSAT), Allen Mouse Brain Atlas, and Mouse Genome Institute (MGI).

Proper citation: Integrated Brain Gene Expression (RRID:SCR_004197) Copy   

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http://www.nephromine.org/

THIS RESOURCE IS NO LONGER IN SERVICE; REPLACED BY NEPHROSEQ; A growing database of publicly available renal gene expression profiles, a sophisticated analysis engine, and a powerful web application designed for data mining and visualization of gene expression. It provides unique access to datasets from the Personalized Molecular Nephrology Research Laboratory incorporating clinical data which is often difficult to collect from public sources and mouse data.

Proper citation: Nephromine (RRID:SCR_003813) Copy   

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http://www.mouseconnectome.org/

Three-dimensional digital connectome atlas of the C57Black/6J mouse brain and catalog of neural tracer injection cases, which will eventually cover the entire brain. Serial sections of each case are available to view at 10x magnification in the interactive iConnectome viewer. The Image Gallery provides a glimpse into some of the highlights of their data set. Representative images of multi-fluorescent tracer labeling can be viewed, while more in depth examination of these and all other cases can be performed in the iConnectome viewer. Phase 1 of this project involves generating a physical map of the basic global wiring diagram by applying proven, state of the art experimental circuit tracing methods systematically, uniformly, and comprehensively to the structural organization of all major neuronal pathways in the mouse brain. Connectivity imaging data for the whole mouse brain at cellular resolution will be presented within a standard 3D anatomic frame available through the website and accompanied by a comprehensive searchable online database. A Phase 2 goal for the future will allow users to view, search, and generate driving direction-like roadmaps of neuronal pathways linking any and all structures in the nervous system. This could be looked on as a pilot project for more ambitious projects in species with larger brains, such as human, and for providing a reliable framework for more detailed local circuitry mapping projects in the mouse.

Proper citation: Mouse Connectome Project (RRID:SCR_004096) Copy   

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http://www.knockoutmouse.org/

Database of the international consortium working together to mutate all protein-coding genes in the mouse using a combination of gene trapping and gene targeting in C57BL/6 mouse embryonic stem (ES) cells. Detailed information on targeted genes is available. The IKMC includes the following programs: * Knockout Mouse Project (KOMP) (USA) ** CSD, a collaborative team at the Children''''s Hospital Oakland Research Institute (CHORI), the Wellcome Trust Sanger Institute and the University of California at Davis School of Veterinary Medicine , led by Pieter deJong, Ph.D., CHORI, along with K. C. Kent Lloyd, D.V.M., Ph.D., UC Davis; and Allan Bradley, Ph.D. FRS, and William Skarnes, Ph.D., at the Wellcome Trust Sanger Institute. ** Regeneron, a team at the VelociGene division of Regeneron Pharmaceuticals, Inc., led by David Valenzuela, Ph.D. and George D. Yancopoulos, M.D., Ph.D. * European Conditional Mouse Mutagenesis Program (EUCOMM) (Europe) * North American Conditional Mouse Mutagenesis Project (NorCOMM) (Canada) * Texas A&M Institute for Genomic Medicine (TIGM) (USA) Products (vectors, mice, ES cell lines) may be ordered from the above programs.

Proper citation: International Knockout Mouse Consortium (RRID:SCR_005574) Copy   

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http://swissregulon.unibas.ch/fcgi/sr/swissregulon

A database of genome-wide annotations of regulatory sites. The predictions are based on Bayesian probabilistic analysis of a combination of input information including: * Experimentally determined binding sites reported in the literature. * Known sequence-specificities of transcription factors. * ChIP-chip and ChIP-seq data. * Alignments of orthologous non-coding regions. Predictions were made using the PhyloGibbs, MotEvo, IRUS and ISMARA algorithms developed in their group, depending on the data available for each organism. Annotations can be viewed in a Gbrowse genome browser and can also be downloaded in flat file format.

Proper citation: SwissRegulon (RRID:SCR_005333) Copy   

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http://fairbrother.biomed.brown.edu/spliceman/index.cgi

An online tool that takes a set of DNA sequences with point mutations and returns a ranked list to predict the effects of point mutations on pre-mRNA splicing. The current implementation includes 11 genomes: human, chimp, rhesus, mouse, rat, dog, cat, chicken, guinea pig, frog and zebrafish.

Proper citation: Spliceman (RRID:SCR_005354) Copy   

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http://the_brain.bwh.harvard.edu/uniprobe/

Database that hosts experimental data from universal protein binding microarray (PBM) experiments (Berger et al., 2006) and their accompanying statistical analyses from prokaryotic and eukaryotic organisms, malarial parasites, yeast, worms, mouse, and human. It provides a centralized resource for accessing comprehensive data on the preferences of proteins for all possible sequence variants ("words") of length k ("k-mers"), as well as position weight matrix (PWM) and graphical sequence logo representations of the k-mer data. The database's web tools include a text-based search, a function for assessing motif similarity between user-entered data and database PWMs, and a function for locating putative binding sites along user-entered nucleotide sequences.

Proper citation: UniPROBE (RRID:SCR_005803) Copy   

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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   

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https://www.eummcr.info/

Embryonic stem cell distribution unit that distributes material arising within European Conditional Mouse Mutagenesis Program consortium, currently targeting vectors and ES cells. Upon user request EUCOMM grow targeting vectors from glycerol stocks and prepare vector DNA. Identity of vector is verified by restriction mapping. Upon user request EUCOMM thaw, expand and re-freeze several aliquots of desired ES cell clone. Standard controls include PCR based assay. Upon additional request EuMMCR unit develops genotyping PCR, which can be used to genotype chimeric mice that may be generated using those ES cell clones.

Proper citation: EuMMCR (RRID:SCR_001506) Copy   

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http://embryo.soad.umich.edu/animal/home.html

THIS RESOURCE IS NO LONGER IN SERVICE, documented on February 14, 2013. A multidimensional, digital atlas based on magnetic resonance images of normal mouse embryos from 9.5 days after conception (E9) to the newborn (P0). The images include surface views and cross-sectional views from the transverse, coronal, and sagittal planes for each embryo. Several movies have also been included to demonstrate growth of the embryos and to present a variety of visualization tools available for studying and documenting embryonic anatomy. These images are organized as a reference for educators and researchers who want to understand better the embryological anatomy of their own specimens and to understand how their images relate to the whole embryo at many stages of development.

Proper citation: Magnetic Resonance Microscopy of Mouse Embryo Specimens (RRID:SCR_001145) Copy   

•   Source: SciCrunch Registry

http://www.genepaint.org/MapE15_5_01.htm

Abbreviated reference atlas for the Embryonic 15.5 post conception day mouse. All sections were nissl stained and digitized. To assist in the initial identification of sites of gene expression sites, maps of brains are available for E15.5, P7 and the adult. These maps depict the boundaries of major brain regions (cortex, thalamus, striatum, globus pallidus, ventral striatum, septum, basal forebrain, hippocampus, midbrain, pons, medulla, cerebellum) and also show the more prominent nerve tracts. Maps are most efficiently used by placing the window depicting the map of interest next to the gene expression image. Browsing between planes of sectioning is permitted thus allowing the most appropriate plane to be selected. The annotation of anatomical details such as brain nuclei is currently beyond the scope of the GenePaint database. Hence, such information on the anatomy of the brain and embryo should be obtained from published atlases of mouse anatomy (Kaufman, 1995; Paxinos and Franklin, 2001; Jacobowitz and Abbott, 1997; Schambra et al., 1992; Valverde1998).

Proper citation: GenePaint E15 Atlas (RRID:SCR_002786) Copy   

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http://neuromab.ucdavis.edu/

A national mouse monoclonal antibody generating resource for biochemical and immunohistochemical applications in mammalian brain. NeuroMabs are generated from mice immunized with synthetic and recombinant immunogens corresponding to components of the neuronal proteome as predicted from genomic and other large-scale cloning efforts. Comprehensive biochemical and immunohistochemical analyses of human, primate and non-primate mammalian brain are incorporated into the initial NeuroMab screening procedure. This yields a subset of mouse mAbs that are optimized for use in brain (i.e. NeuroMabs): for immunocytochemical-based imaging studies of protein localization in adult, developing and pathological brain samples, for biochemical analyses of subunit composition and post-translational modifications of native brain proteins, and for proteomic analyses of native brain protein networks. The NeuroMab facility was initially funded with a five-year U24 cooperative grant from NINDS and NIMH. The initial goal of the facility for this funding period is to generate a library of novel NeuroMabs against neuronal proteins, initially focusing on membrane proteins (receptors/channels/transporters), synaptic proteins, other neuronal signaling molecules, and proteins with established links to disease states. The scope of the facility was expanded with supplements from the NIH Blueprint for Neuroscience Research to include neurodevelopmental targets, the NIH Roadmap for Medical Research to include epigenetics targets, and NIH Office of Rare Diseases Research to include rare disease targets. These NeuroMabs will then be produced on a large scale and made available to the neuroscience research community on an inexpensive basis as tissue culture supernatants or purified immunoglobulin by Antibodies Inc. The UC Davis/NIH NeuroMab Facility makes NeuroMabs available directly to end users and is unable to accommodate sales to distributors for third party distribution. Note, NeuroMab antibodies are now offered through antibodiesinc.

Proper citation: NeuroMab (RRID:SCR_003086) Copy   

•   Source: SciCrunch Registry

http://www.genetrap.org/

Consortium represents all publicly available gene trap cell lines, which are available on non-collaborative basis for nominal handling fees. Researchers can search and browse IGTC database for cell lines of interest using accession numbers or IDs, keywords, sequence data, tissue expression profiles and biological pathways, can find trapped genes of interest on IGTC website, and order cell lines for generation of mutant mice through blastocyst injection. Consortium members include: BayGenomics (USA), Centre for Modelling Human Disease (Toronto, Canada), Embryonic Stem Cell Database (University of Manitoba, Canada), Exchangeable Gene Trap Clones (Kumamoto University, Japan), German Gene Trap Consortium provider (Germany), Sanger Institute Gene Trap Resource (Cambridge, UK), Soriano Lab Gene Trap Resource (Mount Sinai School of Medicine, New York, USA), Texas Institute for Genomic Medicine - TIGM (USA), TIGEM-IRBM Gene Trap (Naples, Italy).

Proper citation: International Gene Trap Consortium (RRID:SCR_002305) Copy   

•   Source: SciCrunch Registry

http://www.genepaint.org/MapP7_01.htm

Abbreviated reference atlas for the P56 mouse. All sections were nissl stained and digitized. To assist in the initial identification of sites of gene expression sites, maps of brains are available for E15.5, P7 and the adult. These maps depict the boundaries of major brain regions (cortex, thalamus, striatum, globus pallidus, ventral striatum, septum, basal forebrain, hippocampus, midbrain, pons, medulla, cerebellum) and also show the more prominent nerve tracts. Maps are most efficiently used by placing the window depicting the map of interest next to the gene expression image. Browsing between planes of sectioning is permitted thus allowing the most appropriate plane to be selected. The annotation of anatomical details such as brain nuclei is currently beyond the scope of the GenePaint database. Hence, such information on the anatomy of the brain and embryo should be obtained from published atlases of mouse anatomy (Kaufman, 1995; Paxinos and Franklin, 2001; Jacobowitz and Abbott, 1997; Schambra et al., 1992; Valverde1998).

Proper citation: GenePaint P7 Atlas (RRID:SCR_002787) Copy   

•   Source: SciCrunch Registry

http://sleep.alleninstitute.org

Collection of gene expression data in mouse brain for five different conditions of sleep and wakefulness to understand sleep deprivation and dynamic changes underlying sleep and wake cycles. Platform to generate cellular resolution expression data.

Proper citation: Allen Institute for Brain Science Sleep Study (RRID:SCR_002983) 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