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

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.

Proper citation: 3D surgical atlases of the murine head (RRID:SCR_008039) 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://homeodb.zoo.ox.ac.uk/

Database of homeobox genes in humans, mice, chickens, frogs, zebrafishes, amphioxuses, fruitflies, beetles, honeybees, and nematodes., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: HomeoDB (RRID:SCR_015492) Copy   

•   Source: SciCrunch Registry

http://catlas.org/mousebrain/#!/

Atlas of gene regulatory elements in adult mouse cerebrum. Atlas of CIS elements, providing information on accessible chromatin in individual cells from regions of adult mouse isocortex, olfactory bulb, hippocampus and cerebral nuclei. Uses resulting data to define candidate cis-regulatory DNA elements in distinct cell groups. Many are linked to putative target genes expressed in diverse cerebral cell types and uncover transcriptional regulators involved in broad spectrum of molecular and cellular pathways in different neuronal and glial cell populations. Used for analysis of gene regulatory programs of mammalian brain and interpretation of non-coding risk variants associated with various neurological disease and traits in humans.

Proper citation: CATlas (RRID:SCR_018690) Copy   

•   Source: SciCrunch Registry

https://portal.brain-map.org/atlases-and-data/rnaseq/mouse-whole-cortex-and-hippocampus-smart-seq

Collection of data set including single cell transcriptomes from multiple cortical areas and hippocampal formation. Samples were collected from dissections of brain regions from  8 week old male and female mice, primarily from pan GABAergic, pan glutamatergic, and pan neuronal transgenic lines, with addition of more specific transgenic lines and some retrogradely labeled cells in VISp and ALM.

Proper citation: Allen Institute Mouse Whole Cortex and Hippocampus SMART-seq (RRID:SCR_019013) Copy   

•   Source: SciCrunch Registry

http://diabetes.wisc.edu/index.php

Interactive database of gene expression and diabetes related clinical phenotypes. Allows to search gene expression in tissues as a function of obesity, strain, and age, in a mouse.

Proper citation: Attie Lab Diabetes Database (RRID:SCR_016639) Copy   

•   Source: SciCrunch Registry

http://mousebrain.org/

Atlas of brain cell types, derived from single cell RNA-Seq data from Linnarsson Lab. Can be browsed by taxon, cell type, tissue, and gene, with information on enriched genes, specific markers, anatomical location and more. Single cell gene expression atlas of mouse nervous system.

Proper citation: mousebrain.org (RRID:SCR_016999) Copy   

•   Source: SciCrunch Registry

https://dfam.org/home

Open collection of Transposable Element DNA sequence alignments, hidden Markov Models, consensus sequences, and genome annotations.Dfam 3.2 provides early access to uncurated, de novo generated families.

Proper citation: Dfam (RRID:SCR_021168) Copy   

•   Source: SciCrunch Registry

http://www.med.umich.edu/tamc/

A service for preparing genetically modified mice and rats for investigators at the University of Michigan. These mice models are typically used to study gene function, gene expression, gene regulation, and for the development of animal models of human disease and gene therapy reagents. TAMC provide access to their micromanipoulation and embryos stem cell workstations along with necessary reagents such as specialized plasmids, embryonic stem (ES) cell lines, FBS, and feeder cells certified for ES cell culture.

Proper citation: Transgenic Animal Model Core (RRID:SCR_000776) Copy   

•   Source: SciCrunch Registry

http://fantom.gsc.riken.jp/4/

The FANTOM consortium is an international collaborative research project initiated and organized by the RIKEN Omics Science Center. In earlier FANTOM efforts we cloned and annotated 103,000 full-length cDNAs from mouse and distributed them to researchers throughout the world. FANTOM1-3 focused on identifying the transcribed components of mammalian cells. This work improved estimates of the total number of genes and their alternative transcript isoforms in both human and mouse, expanded gene families, and revealed that a large fraction of the transcriptome is non-coding. In addition, with the development of Cap Analysis of Gene Expression (CAGE) FANTOM3 could map a large fraction of transcription start sites and revise our models of promoter structure. This updated web resource provides the previous FANTOM results mapped to current genome builds and presents the results of FANTOM4. In FANTOM4 the focus has changed to understanding how these components work together in the context of a biological network. Using deepCAGE (deep sequencing with CAGE) we monitored the dynamics of transcription start site (TSS) usage during a time course of monocytic differentiation in the acute myeloid leukemia cell line THP-1. This allowed us to identify active promoters, monitor their relative expression and define relevant regions for carrying out transcription factor binding site predictions. Computational methods were then used to build a network model of gene expression in this leukemia and the transcription factors key to its regulation. This work gives the first picture of the wiring between genes involved in acute myeloid leukemia and provides a strategy for identifying key factors that determine cell fates. In addition to the network, FANTOM4 data was used in two additional analyses. The first identified a novel class of short RNAs associated with transcription start sites and the second focused on the role of repetitive element expression in the transcriptome. TOOLS *Genome Browser: graphical display of genomic features, such as promoters, exon structures, H3K9 acetylation, transcription factors positioning on the genome, coupled with gene and promoter activities. *EdgeExpressDB: regulatory interactions, such as transcriptional regulation, post-transcriptional silencing with miRNA, and PPI, coupled with gene and promoter activities. *SwissRegulon: FANTOM4 TF regulation is predicted using Motif Activity Response Analysis (MARA) developed by Erik van Nimwegen at Biozentrum. Follow the link to carry out MARA on your own dataset. *Custom Tracks on the UCSC Genome Browser: FANTOM4 tracks on the UCSC Genome Browser Database. *The RIKEN integrated database of mammals: Integration of FANTOM4 data with other mammalian resources, in particular, produced by RIKEN.

Proper citation: FANTOM DB (RRID:SCR_002678) Copy   

•   Source: SciCrunch Registry

http://scicrunch.org/resources

Portal providing identifiers for Antibodies, Model Organisms, and Tools (software, databases, services) created in support of the Resource Identification Initiative, which aims to promote research resource identification, discovery, and reuse. The portal offers a central location for obtaining and exploring Research Resource Identifiers (RRIDs) - persistent and unique identifiers for referencing a research resource. A critical goal of the RII is the widespread adoption of RRIDs to cite resources in the biomedical literature and other places that reference their generation or use. RRIDs use established community identifiers where they exist, and are cross-referenced in their system where more than one identifier exists for a single resource.

Proper citation: Resource Identification Portal (RRID:SCR_004098) Copy   

•   Source: SciCrunch Registry

http://nred.matticklab.com/cgi-bin/ncrnadb.pl

Database of long noncoding RNA expression that integrates annotated expression data from various sources in human and mouse. The database contains both microarray and in situ hybridization data, and supplies a rich tapestry of ancillary information for featured ncRNAs, including evolutionary conservation, secondary structure evidence, genomic context links and antisense relationships.

Proper citation: ncRNA Expression Database (RRID:SCR_008630) Copy   

•   Source: SciCrunch Registry

http://gaa.mpi-bn.mpg.de/

Data analysis service that allows to process CEL files from Affymetrix, Inc. GeneChip Gene 1.0 ST Arrays to identify alternative splicing.

Proper citation: Gene Array Analyzer (RRID:SCR_008323) Copy   

•   Source: SciCrunch Registry

http://genomics.senescence.info/genes/

Collection of annotated and manually curated data of genes related to aging divided into genes related to longevity and/or aging in model organisms (yeast, worms, flies, mice, etc.) and aging related human genes.

Proper citation: GenAge (RRID:SCR_010223) Copy   

•   Source: SciCrunch Registry

https://www.nia.nih.gov/research/dab/aged-rodent-tissue-bank

NIA Aged Rodent Tissue Bank (ARTB) is a repository of tissue collected from mice and rats maintained in the NIA Aged Rodent Colonies. Biospecimens are collected, archived, and distributed under a contractual arrangement with the University of Washington, Seattle. The NIA supports the three R’s of research (Replacement, Reduction, and Refinement) through maximizing the use of existing banked samples from mice and rats and providing tissues for research on aging. Researchers can select frozen tissues, unstained slides from formalin-fixed and paraffin-embedded (FFPE) tissues, or tissue microarrays (TMAs).

Proper citation: NIA Aged Rodent Tissue Bank (RRID:SCR_010607) Copy   

•   Source: SciCrunch Registry

http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=lncBase/index

Database that hosts elaborated information for both predicted and experimentally verified, miRNA-lncRNA interactions. The database consists of two distinct modules. The Experimental Module contains detailed information for more than 5,000 interactions, between 2,958 lncRNAs and 120 miRNAs, ranging from miRNA and lncRNA related facts to information specific to their interaction, the experimental validation methodologies and their outcomes. The Prediction Module, which is based on the latest version of DIANA-microT target prediction algorithm (DIANA-microT-CDS), contains detailed information for more than 10 million interactions, between 56,097 lncRNAs and 3,078 miRNAs, ranging from miRNA and lncRNA related details to specific information regarding their interaction sites, graphical representation of their binding and the predicted score. This module exhibits a unique feature for searching the database. Users are able to add genomic locations to their queries thus browsing every miRNA-lncRNA interaction that has at least one MRE located inside the queried locus.

Proper citation: DIANA-LncBase (RRID:SCR_010840) Copy   

•   Source: SciCrunch Registry

http://www.genomicus.biologie.ens.fr/genomicus-72.01/cgi-bin/search.pl

A genome browser that enables users to navigate in genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time.

Proper citation: Genomicus (RRID:SCR_011791) Copy   

•   Source: SciCrunch Registry

http://gpcr.biocomp.unibo.it/bacello/

A predictor for the subcellular localization of proteins in eukaryotes that is based on a decision tree of several support vector machines (SVMs). It classifies up to four localizations for Fungi and Metazoan proteins and five localizations for Plant ones. BaCelLo's predictions are balanced among different classes and all the localizations are considered as equiprobable.

Proper citation: BaCelLo (RRID:SCR_011965) Copy   

•   Source: SciCrunch Registry

http://web.stanford.edu/group/barres_lab/brain_rnaseq.html

Database containing RNA-Seq transcriptome and splicing data from glia, neurons, and vascular cells of cerebral cortex. Collection of RNA-Seq transcriptome and splicing data from glia, neurons, and vascular cells of mouse cerebral cortex. RNA-Seq of cell types isolated from mouse and human brain.

Proper citation: Brain RNA-Seq (RRID:SCR_013736) Copy   

•   Source: SciCrunch Registry

https://labnodes.vanderbilt.edu/community/profile/id/2228

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 13,2025.Core facility that provides access to isolated pancreatic islets from normal and diabetic models and performs islet functional analysis. The IPA Core also provides solutions for high-resolution whole slide imaging and access to image analysis tools for quantitative assessment of pancreatic islet morphology.

Proper citation: Vanderbilt Diabetes Research and Training Center Islet Procurement and Analysis Core (RRID:SCR_000896) Copy   

•   Source: SciCrunch Registry