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http://www.mbl.org/mbl_main/atlas.html

High-resolution electronic atlases for mouse strains c57bl/6j, a/j, and dba/2j in either coronal or horizontal section. About this Atlas: The anterior-posterior coordinates are taken from an excellent print atlas of a C57BL/6J brain by K. Franklin and G. Paxinos (The Mouse Brain in Stereotaxic Coordinates, Academic Press, San Diego, 1997, ISBN Number 0-12-26607-6; Library of Congress: QL937.F72). The abbreviations we have used to label the sections conform to those in the Franklin-Paxinos atlas. A C57BL/6J mouse brain may contain as many as 75 million neurons, 23 million glial cells, 7 million endothelial cells associated with blood vessels, and 3 to 4 million miscellaneous pial, ependymal, and choroid plexus cells (see data analysis in Williams, 2000). We have not yet counted total cell number in DBA/2J mice, but the counts are probably appreciably lower.The brain and sections were all processed as described in our methods section. The enlarged images have a pixel count of 1865 x 1400 and the resolution is 4.5 microns/pixel for the processed sections.Plans: In the next several years we hope to add several additional atlases of the same sort for other strains of mice. A horizontal C57BL/6J atlas and a DBA/2J coronal atlas were completed by Tony Capra, summer 2000, and additional atlases may be made over the next several years. As describe in the MBL Procedures Section is not hard to make your own strain-specific atlas from the high resolution images in the MBL.

Proper citation: Mouse Brain Atlases (RRID:SCR_007127) Copy   

•   Source: SciCrunch Registry

http://www.cpc.unc.edu/projects/addhealth

Longitudinal study of a nationally representative sample of adolescents in grades 7-12 in the United States during the 1994-95 school year. Public data on about 21,000 people first surveyed in 1994 are available on the first phases of the study, as well as study design specifications. It also includes some parent and biomarker data. The Add Health cohort has been followed into young adulthood with four in-home interviews, the most recent in 2008, when the sample was aged 24-32. Add Health combines longitudinal survey data on respondents social, economic, psychological and physical well-being with contextual data on the family, neighborhood, community, school, friendships, peer groups, and romantic relationships, providing unique opportunities to study how social environments and behaviors in adolescence are linked to health and achievement outcomes in young adulthood. The fourth wave of interviews expanded the collection of biological data in Add Health to understand the social, behavioral, and biological linkages in health trajectories as the Add Health cohort ages through adulthood. The restricted-use contract includes four hours of free consultation with appropriate staff; after that, there''s a fee for help. Researchers can also share information through a listserv devoted to the database.

Proper citation: Add Health (National Longitudinal Study of Adolescent Health) (RRID:SCR_007434) Copy   

•   Source: SciCrunch Registry

http://vox.pharmacology.ucla.edu/home.html

Two-dimensional images of gene expression for 20,000 genes in a coronal slice of the mouse brain at the level of the striatum by using microarrays in combination with voxelation at a resolution of 1 cubic mm gene expression patterns in the brain obtained through voxelation. Voxelation employs high-throughput analysis of spatially registered voxels (cubes) to produce multiple volumetric maps of gene expression analogous to the images reconstructed in biomedical imaging systems.

Proper citation: Voxelation Map of Gene Expression in a Coronal Section of the Mouse Brain (RRID:SCR_008065) Copy   

•   Source: SciCrunch Registry

http://lrpath.ncibi.org/

Web tool to perform gene set enrichment testing. Used to test for predefined biologically relevant gene sets that contain more significant genes from experimental dataset than expected by chance. Logistic regression approach for identifying enriched biological groups in gene expression data.

Proper citation: LRPath (RRID:SCR_018572) Copy   

•   Source: SciCrunch Registry

http://crispr-era.stanford.edu/index.jsp

Software comprehensive design tool for CRISPR mediated gene editing, repression and activation. Fast and comprehensive guide RNA design tool for genome editing, repression and activation. Used for automated genome wide sgRNA design.

Proper citation: CRISPR-ERA (RRID:SCR_018710) Copy   

•   Source: SciCrunch Registry

https://reprint-apms.org/?q=chooseworkflow

Database of Mass Spectrometry contaminants and pipeline for Affinity Purification coupled with Mass Spectrometry analysis. Contaminant repository for affinity purification mass spectrometry data. Database of standardized negative controls. Used to identify protein-protein interactions.

Proper citation: CRAPome (RRID:SCR_025008) Copy   

•   Source: SciCrunch Registry

https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FIRST

Software model based segmentation and registration tool. Used for segmentation of sub-cortical structures. Introduces basic segmentation and vertex analysis for detecting group differences.

Proper citation: FMRIB’s Integrated Registration and Segmentation Tool (RRID:SCR_024921) Copy   

•   Source: SciCrunch Registry

http://www.emouseatlas.org

Detailed multidimensional digital multimodal atlas of C57BL/6J mouse nervous system with data and informatics pipeline that can automatically register, annotate, and visualize large scale neuroanatomical and connectivity data produced in histology, neuronal tract tracing, MR imaging, and genetic labeling. MAP2.0 interoperates with commonly used publicly available databases to bring together brain architecture, gene expression, and imaging information into single, simple interface.Resource to visualise mouse development, identify anatomical structures, determine developmental stage, and investigate gene expression in mouse embryo. eMouseAtlas portal page allows access to EMA Anatomy Atlas of Mouse Development and EMAGE database of gene expression.EMAGE is freely available, curated database of gene expression patterns generated by in situ techniques in developing mouse embryo. EMA, e-Mouse Atlas, is 3-D anatomical atlas of mouse embryo development including histology and includes EMAP ontology of anatomical structure, provides information about shape, gross anatomy and detailed histological structure of mouse, and framework into which information about gene function can be mapped.

Proper citation: eMouseAtlas (RRID:SCR_002981) Copy   

•   Source: SciCrunch Registry

https://confluence.crbs.ucsd.edu/display/NIF/DRG

Gene expression data from published journal articles that test hypotheses relevant to neuroscience of addiction and addictive behavior. Data types include effects of particular drug, strain, or knock out on particular gene, in particular anatomical region. Focuses on gene expression data and exposes data from investigations using DNA microarrays, polymerase chain reaction, immunohistochemistry and in-situ hybridizations. Data are available for query through NIF interface.Data submissions are welcome.

Proper citation: Drug Related Gene Database (RRID:SCR_003330) Copy   

•   Source: SciCrunch Registry

https://rrid.site/rin/sources/SCR_005400

Interactive portal for finding and submitting biomedical resources. Resources within SciCrunch have assigned RRIDs which are used to cite resources in scientific manuscripts. SciCrunch Registry, formerly NIF Registry, provides resources catalog. Allows to add new resources. Allows edit existing resources after registration. Curators are tasked with identifying and registering resources, examining data, writing configuration files to index and display data and keeping contents current.

Proper citation: SciCrunch Registry (RRID:SCR_005400) Copy   

•   Source: SciCrunch Registry

http://biositemaps.ncbcs.org/rds/search.html

Resource Discovery System is a web-accessible and searchable inventory of biomedical research resources. Powered by the Resource Discovery System (RDS) that includes a standards-based informatics infrastructure * Biositemaps Information Model * Biomedical Resource Ontology Extensions * Web Services distributed web-accessible inventory framework * Biositemap Resource Editor * Resource Discovery System Source code and project documentation to be made available on an open-source basis. Contributing institutions: University of Pittsburgh, University of Michigan, Stanford University, Oregon Health & Science University, University of Texas Houston. Duke University, Emory University, University of California Davis, University of California San Diego, National Institutes of Health, Inventory Resources Working Group Members

Proper citation: Resource Discovery System (RRID:SCR_005554) Copy   

•   Source: SciCrunch Registry

http://www.exocarta.org/

Manually curated database of exosomal proteins, RNA and lipids. Web based compendium of exosomal cargo. Database catalogs information from both published and unpublished exosomal studies. Mode of exosomal purification and characterization, biophysical and molecular properties are listed.

Proper citation: ExoCarta (RRID:SCR_021960) Copy   

•   Source: SciCrunch Registry

http://courses.jax.org/2012/addiction.html

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. This course emphasizes genetic applications and approaches to drug addiction research through methodological instruction based on literature, data sets and informatics resources drawn from studies of addiction related phenotypes. The course includes plenary sessions on major progress in addiction genetics, and discussion sessions in which students present their work for discussion on applications of genetic methods. Students will leave the course able to design and interpret genetic and genomic studies of addiction as they relate to their specific research question, and will be able to make use of current bioinformatics resources to identify research resources and make use of public data sources in their own research.

Proper citation: Short Course on the Genetics of Addiction (RRID:SCR_005560) Copy   

•   Source: SciCrunch Registry

https://github.com/calico/borzoi

Software package to access the Borzoi models, which are convolutional neural networks trained to predict RNA-seq coverage at 32bp resolution given 524kb input sequences.

Proper citation: Borzoi (RRID:SCR_026619) Copy   

•   Source: SciCrunch Registry

https://emberarchive.org/

BRAIN Initiative data archive for multi-modal neurophysiological and behavioral data, supporting the Brain Behavior Quantification and Synchronization (BBQS) Program. Accessible and versatile data archive for storage, processing, and curation of multimodal neurophysiological and behavioral datasets. EMBER extends established BRAIN Initiative data infrastructure, provides new data harmonization and synchronization capabilities, and supports scalable integrations for data coordination and AI driven batch processing to enable the goals of the BBQS program.

Proper citation: Ecosystem for Multi-modal Brain-behavior Experimentation and Research (RRID:SCR_026700) Copy   

•   Source: SciCrunch Registry