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on page 1 showing 20 out of 547 results

    3DBar

Cite this (3DBar, RRID:SCR_008896)

URL: http://www.3dbar.org

Resource Type: Resource, production service resource, analysis service resource, reference atlas, software resource, service resource, atlas, data or information resource

Software package for reconstructing three-dimensional models of brain structures from 2-D delineations using a customizable and reproducible workflow. 3dBAR also works as an on-line service (http://service.3dbar.org) offering a variety of functions for the hosted datasets: * downloading reconstructions of desired brain structures in predefined quality levels in various supported formats as well as created using customizable settings, * previewing models as bitmap thumbnails and (for webGL enabled browsers) interactive manipulation (zooming, rotating, etc.) of the structures, * downloading slides from available datasets as SVG drawings. 3dBAR service can also be used by other websites or applications to enhance their functionality. * Operating System: Linux * Programming Language: Python * Supported Data Format: NIfTI-1, Other Format, VRML

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Cite this (3D MRI Atlas of Mouse Development, RRID:SCR_008090)

URL: http://mouseatlas.caltech.edu/

Resource Type: Resource, atlas, data or information resource

A 3D digital atlas of normal mouse development constructed from magnetic resonance image data. The download is a zipped file containing the six atlases Theiler Stages (ts) 13, 21,23, 24, 25 and 26 and MRI data for an unlabeled ts19 embryo. To view the atlases, download and install MBAT from: http://mbat.loni.ucla.edu Specimens were prepared in aqueous, isotonic solutions to avoid tissue shrinkage. Limited specimen handling minimized physical perturbation of the embryos to ensure accurate geometric representations of developing mouse anatomy. Currently, the atlas contains orthogonal sections through MRI volumes, three stages of embryos that have annotated anatomy, photographs of several stages of development, lineage trees for annotated embryos and a gallery of images and movies derived from the annotations. Anatomical annotations can be viewed by selecting a transverse section and selecting a pixel on the displayed slice.

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Cite this (3D surgical atlases of the murine head, RRID:SCR_008039)

URL: http://phm.utoronto.ca/~jeffh/surgical.htm

Resource Type: Resource, atlas, data or information resource

3D interactive atlas of two mouse brains, 129S1/SvImJ and C57Bl/6J. The aim of this resource is to enhance comparative morphometric analyses and stereotactic surgical procedures in mice. These representations of the murine brain and skull, in conjunction with the resource''s development of a new, more dynamic master coordinate system, provide improved accuracy with respect to targeting CNS structures during surgery compared with previous systems. The interactive three-dimensional nature of these atlases also provide users with stereotactic information necessary to perform accurate off-axis surgical procedures, as is commonly required for experiments such as in vivo micro-electroporation. In addition, three-dimensional analysis of the brain and skull shape in C57Bl, 129Sv, CD1, and additional murine strains, suggests that a stereotactic coordinate system based upon the lambda and rostral confluence of the sinuses at the sagittal midline, provides improved accuracy compared with the traditional lambdabregma landmark system. These findings demonstrate the utility of developing highly accurate and robust three-dimensional representations of the murine brain and skull, in which experimental outputs can be directly compared using a unified coordinate system.

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Cite this (ABA Adult Mouse Brain Ontology, RRID:SCR_010286)

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

Resource Type: Resource, ontology, data or information resource, controlled vocabulary

Allen Brain Atlas P56 Mouse Ontology

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    Abgent

Cite this (Abgent, RRID:SCR_008393)

URL: http://abgent.com

Resource Type: Resource, antibody supplier, core facility, service resource, access service resource, reagent supplier, material resource

An antibody supplier and core facility.

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Cite this (ABS: A Database of Annotated Regulatory Binding Sites From Orthologous Promoters, RRID:SCR_002276)

URL: http://genome.imim.es/datasets/abs2005/index.html

Resource Type: Resource, data or information resource, database

Public database of known binding sites identified in promoters of orthologous vertebrate genes that have been manually curated from bibliography. We have annotated 650 experimental binding sites from 68 transcription factors and 100 orthologous target genes in human, mouse, rat or chicken genome sequences. Computational predictions and promoter alignment information are also provided for each entry. For each gene, TFBSs conserved in orthologous sequences from at least two different species must be available. Promoter sequences as well as the original GenBank or RefSeq entries are additionally supplied in case of future identification conflicts. The final TSS annotation has been refined using the database dbTSS. Up to this release, 500 bps upstream the annotated transcription start site (TSS) according to REFSEQ annotations have been always extracted to form the collection of promoter sequences from human, mouse, rat and chicken. For each regulatory site, the position, the motif and the sequence in which the site is present are available in a simple format. Cross-references to EntrezGene, PubMed and RefSeq are also provided for each annotation. Apart from the experimental promoter annotations, predictions by popular collections of weight matrices are also provided for each promoter sequence. In addition, global and local alignments and graphical dotplots are also available.

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    AceView

Cite this (AceView, RRID:SCR_002277)

URL: http://www.ncbi.nlm.nih.gov/ieb/research/acembly/

Resource Type: Resource, data or information resource, database

THIS RESOURCE IS NO LONGER SUPPORTED, documented August 29, 2016. AceView offers an integrated view of the human, nematode and Arabidopsis genes reconstructed by co-alignment of all publicly available mRNAs and ESTs on the genome sequence. Our goals are to offer a reliable up-to-date resource on the genes and their functions and to stimulate further validating experiments at the bench. AceView provides a curated, comprehensive and non-redundant sequence representation of all public mRNA sequences (mRNAs from GenBank or RefSeq, and single pass cDNA sequences from dbEST and Trace). These experimental cDNA sequences are first co-aligned on the genome then clustered into a minimal number of alternative transcript variants and grouped into genes. Using exhaustively and with high quality standards the available cDNA sequences evidences the beauty and complexity of mammals' transcriptome, and the relative simplicity of the nematode and plant transcriptomes. Genes are classified according to their inferred coding potential; many presumably non-coding genes are discovered. Genes are named by Entrez Gene names when available, else by AceView gene names, stable from release to release. Alternative features (promoters, introns and exons, polyadenylation signals) and coding potential, including motifs, domains, and homologies are annotated in depth; tissues where expression has been observed are listed in order of representation; diseases, phenotypes, pathways, functions, localization or interactions are annotated by mining selected sources, in particular PubMed, GAD and Entrez Gene, and also by performing manual annotation, especially in the worm. In this way, both the anatomy and physiology of the experimentally cDNA supported human, mouse and nematode genes are thoroughly annotated. Our goals are to offer an up-to-date resource on the genes, in the hope to stimulate further experiments at the bench, or to help medical research. AceView can be queried by meaningful words or groups of words as well as by most standard identifiers, such as gene names, Entrez Gene ID, UniGene ID, GenBank accessions.

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    ADaCGH

Cite this (ADaCGH, RRID:SCR_010916)

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

Resource Type: Resource, analysis service resource, software resource, data analysis service, service resource, production service resource

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/

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    ADGO

Cite this (ADGO, RRID:SCR_006343)

URL: http://www.btool.org/ADGO2

Resource Type: Resource, analysis service resource, data analysis service, service resource, production service resource

A web-based tool that provides composite interpretations for microarray data comparing two sample groups as well as lists of genes from diverse sources of biological information. It provides multiple gene set analysis methods for microarray inputs as well as enrichment analyses for lists of genes. It screens redundant composite annotations when generating and prioritizing them. It also incorporates union and subtracted sets as well as intersection sets. Users can upload their gene sets (e.g. predicted miRNA targets) to generate and analyze new composite sets.

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Cite this (Adult Mouse Anatomy Ontology, RRID:SCR_006568)

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

Resource Type: Resource, ontology, data or information resource, controlled vocabulary

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.

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Cite this (Aged Rodent Tissue Arrays, RRID:SCR_007332)

URL: http://www.nia.nih.gov/research/dab/aged-rodent-tissue-bank-handbook/tissue-arrays

Resource Type: Resource, biomaterial analysis service, analysis service resource, service resource, production service resource, material analysis service

Offer high-throughput analysis of tissue histology and protein expression for the biogerontology research community. Each array is a 4 micron section that includes tissue cores from multiple tissues at multiple ages on one slide. The arrays are made from ethanol-fixed tissue and can be used for all techniques for which conventional tissue sections can be used. Ages are chosen to span the life from young adult to very old age. (available ages: 4, 12, 18, 24 and 28 months of age) Images of H&E stained punches are available for Liver, Cardiac Muscle, and Brain. The NIA aged rodent tissue arrays were developed with assistance from the National Cancer Institute (NCI) Tissue Array Research Program (TARP), led by Dr. Stephen Hewitt, Director. NCI TARP contains more information on tissue array construction, protocols for using arrays, and references. Preparation and Product Description Tissue arrays are prepared in parallel from different sets of animals so that experiments can be conducted in duplicate, with each array using unique animals with a unique product number. The product descriptions page describes each array, including: * Strain * Gender * Ages * Tissues * Animal Identification Numbers

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Cite this (Aged Rodent Tissue Bank, RRID:SCR_010607)

URL: http://www.nia.nih.gov/research/dab/aged-rodent-tissue-bank-handbook

Resource Type: Resource, biomaterial supply resource, material resource, tissue bank

A repository of tissue collected from the NIA Aged Rodent Colonies under contractual arrangement with BioReliance. The NIA colonies are barrier maintained and Specific Pathogen Free. Tissues are fresh frozen and stored at -80 degrees Celsius. Tissue from the NIA Aged Rodent Tissue Bank is available to investigators at academic and nonprofit research institutions who are engaged in funded research on aging. The project name and source of funding must accompany all orders. It may not be possible to ship tissue to foreign countries that have restrictions on the import of animal tissues or products. Please Note: Incomplete order forms will be returned. We can only offer following week delivery for those orders for which completed order forms are received by the deadline of Tuesday noon, Eastern time. Starting April 1, 2012, a copy (.pdf) of the purchase order must be emailed along with the order form.

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    aGEM

Cite this (aGEM, RRID:SCR_013349)

URL: http://agem.cnb.csic.es/VisualOmics/aGEM/

Resource Type: Resource, data or information resource, database

Database platform of an integrated view of eight databases (mouse gene expression resources: EMAGE, GXD, GENSAT, BioGPS, ABA, EUREXPRESS; human gene expression databases: HUDSEN, BioGPS and Human Protein Atlas) that allows the experimentalist to retrieve relevant statistical information relating gene expression, anatomical structure (space) and developmental stage (time). Moreover, general biological information from databases such as KEGG, OMIM and MTB is integrated too. It can be queried using gene and anatomical structure. Output information is presented in a friendly format, allowing the user to display expression maps and correlation matrices for a gene or structure during development. An in-depth study of a specific developmental stage is also possible using heatmaps that relate gene expression with anatomical components. This is a powerful tool in the gene expression field that makes easy the access to information related to the anatomical pattern of gene expression in human and mouse, so that it can complement many functional genomics studies. The platform allows the integration of gene expression data with spatial-temporal anatomic data by means of an intuitive and user friendly display.

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Cite this (Aging Cell Repository, RRID:SCR_007320)

URL: http://ccr.coriell.org/nia/

Resource Type: Resource, database, biomaterial supply resource, biospecimen repository, service resource, storage service resource, cell repository, material storage repository, material resource, data or information resource

A cell repository containing cells and DNA for studies of aging and the degenerative processes associated with it. Scientists use the highly-characterized, viable, and contaminant-free cell cultures from this collection for research on such diseases as Alzheimer's disease, progeria, Parkinson's disease, Werner syndrome, and Cockayne syndrome. The collections of the Repository include DNA and cell cultures from individuals with premature aging disorders, as well as DNA from individuals of advanced age from the the Baltimore Longitudinal Study of Aging at the Gerontology Research Center and other Longevity Collections. The Repository also includes samples from an Adolescent Study of Obesity, Apparently Healthy Controls, Animal Models of Aging, and both human and animal differentiated cell types. The cells in this resource have been collected over the past three decades using strict diagnostic criteria and banked under the highest quality standards of cell culture. Scientists can use the highly-characterized, viable, and contaminant-free cell cultures from this collection for genetic and cell biology research.

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Cite this (Aging Genes and Interventions Database, RRID:SCR_002701)

URL: http://uwaging.org/genesdb/

Resource Type: Resource, service resource, data or information resource, data repository, storage service resource, database

A database of genes and interventions connected with aging phenotypes including those with respect to their effects on life-span or age-related neurological diseases. Information includes: organism, aging phenotype, allele type, strain, gene function, phenotypes, mutant, and homologs. If you know of published data (or your own unpublished data that you'd like to share) not currently in the database, please use the Submit a Gene/Intervention link.

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    ALEA

Cite this (ALEA, RRID:SCR_006417)

URL: http://www.bcgsc.ca/platform/bioinfo/software/alea

Resource Type: Resource, software resource, software toolkit

A computational software toolbox for allele-specific (AS) epigenomics analysis. It incorporates allelic variation data within existing resources, allowing for the identification of significant associations between epigenetic modifications and specific allelic variants in human and mouse cells. It provides a customizable pipeline of command line tools for AS analysis of next-generation sequencing data (ChIP-seq, RNA-seq, etc.) that takes the raw sequencing data and produces separate allelic tracks ready to be viewed on genome browsers. ALEA takes advantage of the available genomic resources for human (The 1000 Genomes Project Consortium) and mouse (The Mouse Genome Project) to reconstruct diploid in-silico genomes for human or hybrid mice under study. Then, for each accompanying ChIP-seq or RNA-seq dataset, it generates two Wiggle track format (WIG) files from short reads aligned differentially to each haplotype.

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Cite this (Allen Brain Atlas API, RRID:SCR_005984)

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

Resource Type: Resource, software resource, software application, source code

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

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Cite this (Allen Developing Mouse Brain Atlas, RRID:SCR_002990)

URL: http://developingmouse.brain-map.org/

Resource Type: Resource, atlas, database, expression atlas, reference atlas, data or information resource

A map of gene expression in the developing mouse brain revealing gene expression patterns from embryonic through postnatal stages as well as provides information about both spatial and temporal regulation of gene expression - now offering over 1,000 genes and new anatomic reference atlases. The Allen Developing Mouse Brain Atlas provides a characterization of gene expression in the brain beginning with mid-gestation through to juvenile/young adult. Building upon the foundation established by the original Allen Mouse Brain Atlas, the Allen Developing Mouse Brain Atlas provides a framework to explore temporal and spatial regulation of gene expression, effectively a 4D atlas, with a highly accessible and easily navigable free online database. When complete, this Atlas will extend the Allen Mouse Brain Atlas by offering gene expression data across seven new developmental stages. An application has been created to enable viewing of this data set, complete with tools for search and navigation of the data. As of the April 2009 release, 1,000 unique genes are available covering seven stages of the developmental process. Feature highlights in this release include seven sagittal reference atlases created with a developmental ontology. These anatomic atlases, currently available through Level 05, may be viewed alongside the in situ hybridization (ISH) data as well as by itself. Additional in situ hybridization data, further reference atlas detail and additional search and navigation tools will be provided in future releases.

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Cite this (Allen Institute for Brain Science, RRID:SCR_006491)

URL: http://www.brain-map.org

Resource Type: Resource, atlas, topical portal, portal, data or information resource

Independent 501(c)(3) nonprofit medical research organization dedicated to accelerating the understanding of how the human brain works. Utilizing the mouse model system, a multidisciplinary group of neuroscientists, molecular biologists, informaticists, engineers, mathematicians, statisticians, and computational biologists have joined together to investigate expression of 20,000 genes in the adult mouse brain and to map gene expression to a cellular level beyond neuroanatomic boundaries. The data generated from this joint effort is contained in the publicly available Allen Brain Atlas application. Molecular approaches to understanding the functional organization of the brain promise new insights into the relationships between genes, brain, behavior and disease. To facilitate such insights, the Allen Institute produces large-scale projects and makes the resulting data and tools freely available online to scientists worldwide. These open resources, all available at www.brain-map.org, are intended to foster scientific discovery and collaboration. Atlases: Allen Developing Mouse Brain Atlas: A map of gene expression in the developing mouse brain. Building on the Allen Mouse Brain Atlas, this atlas reveals gene expression patterns from embryonic through postnatal stages to provide information about both spatial and temporal regulation of gene expression. Allen Spinal Cord Atlas: A genome-wide map of gene expression throughout the adult and juvenile mouse spinal cord. The Atlas was made possible through the generous support of a diverse consortium of funders, representing disease organizations, foundations, and corporate and private donors. Allen Mouse Brain Atlas (formerly Allen Brain Atlas): A genome-wide, three-dimensional map of gene expression in the adult mouse brain. Similar in scale to the Human Genome Project, the Atlas reveals the expression patterns of approximately 20,000 genes throughout the entire adult mouse brain down to the cellular level. The Allen Institutes inaugural project, the Atlas was completed in 2006. Studies: Mouse Diversity Study: Characterization of gene expression in the brain across genetic backgrounds and sex. Expanding on the Allen Mouse Brain Atlas, this resource includes data for 49 pharmaceutical drug target genes and a selected set of additional genes across seven mouse strains and in female mice. Transgenic Mouse Study: Comprehensive characterization of the expression patterns of genetically-controlled markers or tool genes in the brains of transgenic mice. Providing standardized, detailed, anatomical profiling of transgene expression throughout the brain, this dataset is intended to reveal the potential of each transgenic mouse line and help researchers choose the appropriate tools for their studies. Human Cortex Study: A collection of gene expression data in the adult human neocortex. Providing data for several categories of genes across different cortical regions and human individuals, including control and schizophrenic cases, the dataset has the potential to enable exploration of variability in cortical gene expression across different ages, between genders across different regions of the cortex and in schizophrenia. Sleep Study: A comprehensive collection of gene expression data in the mouse brain for five different conditions of sleep and wakefulness. Generated in collaboration with SRI International, this unique dataset is intended to help sleep researchers advance understanding of sleep deprivation and the dynamic changes underlying sleep/wake cycles. The sleep study was funded by an award from the U.S. Department of Defense.

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Cite this (Allen Institute for Brain Science Sleep Study, RRID:SCR_002983)

URL: http://sleep.alleninstitute.org

Resource Type: Resource, data set, atlas, data or information resource

A comprehensive collection of gene expression data in the mouse brain for five different conditions of sleep and wakefulness. Generated in collaboration with SRI International, this unique dataset is intended to help sleep researchers advance understanding of sleep deprivation and the dynamic changes underlying sleep/wake cycles. A high-throughput colorimetric in situ hybridization platform has been used to generate cellular resolution expression data for over 200 genes. In addition, microarray data for seven brain regions from the same five experimental conditions are downloadable from the web site; and difference grids are available for viewing differences between conditions in 3-D using Brain Explorer. Sleep deprivation leads to a repertoire of cognitive, attentional and emotional deficits that are seriously detrimental in occupations requiring alertness. These deficits may be associated with changes in gene expression in specific regions of the brain. The Allen Institute is in the process of generating a collection of cellular resolution data for gene expression in the mouse brain in response to sleep deprivation and sleep state. Using the Allen Institute high throughput in situ hybridization platform, gene expression has been examined under five experimental conditions in mice in collaboration with SRI International, and the images are presented online as a resource for sleep researchers. Sleep conditions include: Sleep-deprived for 6 hours; Time of day control for sleep-deprivation; Recovery sleep (4 hours) following 6 hours of sleep deprivation; Time of day control for recovery sleep; and waking. Project data is available in the following formats: Colorimetric ISH and Nissl images for 224 genes across 5 conditions, some with replicates Microarray data for 7 brain regions across 5 conditions Difference grids for viewing differences between conditions in 3-D using Brain Explorer Microarray data is available for seven brain regions collected from five experimental conditions: sleep deprivation, recovery sleep, and three time-of-day controls. The brain regions include four regions associated with sleep-wake regulation or circadian rhythm: suprachiasmatic nucleus, locus coeruleus, tuberomammillary nucleus and lateral hypothalamus in the vicinity of the hypocretin neurons. In order to assess the effect of sleep deprivation on gene expression in regions potentially involved in mood, memory, or executive function, an additional three brain regions were analyzed by microarray: orbital cortex, cortical amygdala (posteromedial), and dorsal entorhinal cortex. 140 microarray files are available for download in text, Codelink, and Rosetta Resolver file formats. Difference Grids allow the user to navigate changes in gene expression for a given gene across two experimental conditions, such as sleep deprivation compared to its time of day control. Difference grids are available for genes which have been assayed in replicate by ISH.

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