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http://uwaging.org/genesdb/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 17,2023. 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 If you know of published data (or your own unpublished data that you'd like to share) not currently in the database, please use the Submit a Gene/Intervention link.

Proper citation: Aging Genes and Interventions Database (RRID:SCR_002701) Copy   

•   Source: SciCrunch Registry

http://bioweb.ensam.inra.fr/esther

Database and tools for analysis of protein and nucleic acid sequences belonging to superfamily of alpha/beta hydrolases homologous to cholinesterases. Covers multiple species, including human, mouse caenorhabditis and drosophila., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: ESTHER (RRID:SCR_002621) Copy   

•   Source: SciCrunch Registry

http://www.gudmap.org/Resources/Ontologies.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. A high-resolution ontology has been developed by members of the GUDMAP consortium to describe the subcompartments of the developing murine genitourinary tract. This ontology incorporates what can be defined histologically and begins to encompass other structures and cell types already identified at the molecular level. The GUDMAP ontology encompasses Theiler stage (TS) 17-27 of development as well as the sexually mature adult. It has been written as a partonomic, text-based, hierarchical ontology that, for the embryological stages, has been developed as a high-resolution expansion of the existing Edinburgh Mouse Atlas Project (EMAP) ontology. It also includes group terms for well-characterized structural and/or functional units comprising several sub-structures, such as the nephron and juxtaglomerular complex. Each term has been assigned a unique identification number. Synonyms have been used to improve the success of query searching and maintain wherever possible existing EMAP terms relating to this organ system.

Proper citation: GUDMAP Ontology (RRID:SCR_002637) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/CCDS/

Database (anonymous FTP) resulting from a collaborative effort to identify a core set of human and mouse protein coding regions that are consistently annotated and of high quality. The long term goal is to support convergence towards a standard set of gene annotations. Collaborators are EBI, NCBI, UCSC, WTSI and the initial results are also available from the participants'''' genome browser Web sites. In addition, CCDS identifiers are indicated on the relevant NCBI RefSeq and Entrez Gene records and in Map Viewer displays of RNA (RefSeq) and Gene annotations on the reference assembly.

Proper citation: Consensus CDS (RRID:SCR_006729) Copy   

•   Source: SciCrunch Registry

http://epgd.biosino.org/SysZNF/

THIS RESOURCE IS NO LONGER IN SERVICE, documented September 2, 2016. SysZNF is an information resource for C2H2 Zinc Finger genes in humans and mice. C2H2 Zinc Finger genes (C2H2-ZNF) constitute the largest class of transcription factors in humans and mouse. C2H2 zinc finger proteins primarily bind to DNA. In most cases, they attach to regions near certain genes and turn the genes on and off as needed. The researches on these genes show light on the evolution of gene regulation systems and development. Therefore, we develop SysZNF (Systematical information resource of Zinc Finger genes) to collect the information related to C2H2 Zinc Finger genes. The aim of SysZNF was to provide a user-friendly interface for rendering the information (DNA, Expression, Protein, Reference and so on) of each C2H2-ZNF (e.g., ZNF10) and to enable a comprehensive analysis of C2H2-ZNF. This project was supported by the Proteome-Center at Rostock University (PCRU) who conceives the concept of the database and Key laboratory of Systems biology at the Shanghai Institute for Biological Sciences (SIBS) who implemented the database. It is maintained jointly by PCRU and SIBS.

Proper citation: SysZNF - C2H2 Zinc Finger genes (RRID:SCR_007056) Copy   

•   Source: SciCrunch Registry

https://www.embrys.jp/embrys/html/About.html

Data collection of gene expression patterns mapped in whole-mount mouse embryo (ICR strain) of mid-gestational stages (Embryonic Day 9.5, 10.5, 11.5), in which most striking dynamics in pattern formation and organogenesis is observed. Collection of gene expression patterns of transcription factors (TFs) and TF-related factors such as transcription cofactors. Genes were extracted from databases including RIKEN Transcription Factor Database and Panther Classification System.

Proper citation: EMBRYS (RRID:SCR_006689) Copy   

•   Source: SciCrunch Registry

http://mousespinal.brain-map.org/about.html

Platform for exploring spinal cord at cellular and molecular levels. Map of gene expression for adult and juvenile mouse spinal cord. Provides map of normal mouse when used to compare gene expression in diseased or injury models. Interactive database of gene expression mapped across all anatomic segments of mouse spinal cord at postnatal days 4 and 56. Indexed set of images based on RNA in situ hybridization data, searchable and sortable by gene, age, expression, cervical, thoracic, lumbar, sacral, and coccygeal segments.

Proper citation: Allen Mouse Spinal Cord Atlas (RRID:SCR_007418) Copy   

•   Source: SciCrunch Registry

http://germsage.nichd.nih.gov

Collection of male germ cell transcriptiome information derived from Serial Analysis of Gene Expression (SAGE). It includes the three key germ cell stages in spermatogenesis, including mouse type A spermatogonia (Spga), pachytene spermatocytes (Spcy), and round spermatids (Sptd). A total of 452,095 SAGE tags are represented in all the libraries and is by far the most comprehensive resource available. Users can choose a global view of germ cell transcriptome data in the UCSC Genome browser. They can also search genes or specify searching criteria based on tag sequence, chromosomal location or tag counts.

Proper citation: GermSAGE (RRID:SCR_007689) Copy   

•   Source: SciCrunch Registry

http://mirgator.kobic.re.kr/

Database of compiled, public, deep sequencing miRNA data and several novel tools to facilitate exploration of massive data. The miR-seq browser supports users to examine short read alignment with the secondary structure and read count information available in concurrent windows. Features such as sequence editing, sorting, ordering, import and export of user data are of great utility for studying iso-miRs, miRNA editing and modifications. miRNA����??target relation is essential for understanding miRNA function. Coexpression analysis of miRNA and target mRNAs, based on miRNA-seq and RNA-seq data from the same sample, is visualized in the heat-map and network views where users can investigate the inverse correlation of gene expression and target relations, compiled from various databases of predicted and validated targets.

Proper citation: miRGator (RRID:SCR_007793) Copy   

•   Source: SciCrunch Registry

http://www.chibi.ubc.ca/Gemma

Resource for reuse, sharing and meta-analysis of expression profiling data. Database and set of tools for meta analysis, reuse and sharing of genomics data. Targeted at analysis of gene expression profiles. Users can search, access and visualize coexpression and differential expression results.

Proper citation: Gemma (RRID:SCR_008007) Copy   

•   Source: SciCrunch Registry

http://polya.umdnj.edu/

A database of mRNA polyadenylation sites. PolyA_DB version 1 contains human and mouse poly(A) sites that are mapped by cDNA/EST sequences. PolyA_DB version 2 contains poly(A) sites in human, mouse, rat, chicken and zebrafish that are mapped by cDNA/EST and Trace sequences. Sequence alignments between orthologous sites are available. PolyA_SVM predicts poly(A) sites using 15 cis elements identified for human poly(A) sites.

Proper citation: PolyA DB (RRID:SCR_007867) Copy   

•   Source: SciCrunch Registry

http://www.brainnav.com

THIS RESOURCE IS NO LONGER IN SERVICE, documented December 31, 2013. An interactive atlas and 3D brain software for research, structure analysis, and education, it offers six atlases representing four species: the mouse, rat, monkey and human. The stereotaxic coordinates atlases are available for all four species and the rodent models have additional chemoarchitectonic atlases. BrainNavigator helps locate specific areas of the brain, making visualizing and experimental planning in the brain easier. *Plan: Browse 6 Atlases, Visualize with 3D models, Search Literature, Analyze gene expression, Identify connections *Publish: Access reference tools, Use and print images for publication, Search literature *Propose: Use and print images for proposals, Search literature, Locate gene expression in 2D and 3D, Identify connections *Produce: Simulate injections, Customize new coordinates, virtually slice sections, overlay atlas maps on your own images, create personal atlas maps With BrainNavigator, you''ll gain 24/7 access to their powerful 3D brain interactive software tool that helps further research in the neurosciences. In addition, their vast library of widely respected and referenced brain publications will provide a plethora of information on the most current brain research available. As publisher of the gold standard in brain atlas publications authored by the team around the leading brain cartographers George Paxinos and Charles Watson, they are pleased to bring an advanced tool to today''s neuroscientists and educators. Combining atlas content and 3D capabilities based on technologies from the Allen Institute for Brain Science, this online workflow solution brings brain research, analysis and education tools to your fingertips.

Proper citation: BrainNavigator (RRID:SCR_008289) Copy   

•   Source: SciCrunch Registry

http://opossum.cisreg.ca

A web-based system for the detection of over-represented conserved transcription factor binding sites and binding site combinations in sets of genes or sequences.

Proper citation: oPOSSUM (RRID:SCR_010884) Copy   

•   Source: SciCrunch Registry

http://annmap.picr.man.ac.uk/

A genome browser that includes mappings between genomic features and Affymetrix microarrays. Associated with annmap is: * a Bioconductor package, annmap that provides programmatic access to the underlying MySQL database tables (which are freely available for download on this site) * xmapbridge, a Bioconductor package that outputs numeric data in a form suitable for presentation in the browser. This is supported by XMapBridge, a Java client that sits on the local desktop and performs the graph rendering for the browser.

Proper citation: Annmap (RRID:SCR_011783) Copy   

•   Source: SciCrunch Registry

http://mitobreak.portugene.com/cgi-bin/Mitobreak_home.cgi

Database with curated datasets of mitochondrial DNA (mtDNA) rearrangements. Users may submit new mtDNA rearrangements.

Proper citation: MitoBreak (RRID:SCR_012949) Copy   

•   Source: SciCrunch Registry

http://www.rcsb.org/#Category-welcome

Collection of structural data of biological macromolecules. Database of information about 3D structures of large biological molecules, including proteins and nucleic acids. Users can perform queries on data and analyze and visualize results.

Proper citation: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) (RRID:SCR_012820) Copy   

•   Source: SciCrunch Registry

http://www.scienceexchange.com/facilities/anti-infectives-screening-and-insectary-core-facilities-nyu

Our insectary produces five rodent malaria strains weekly and will ship live sporozoite infected Anopheles stephensi to investigators for research use (Plasmodium berghei GFP, luciferase or red-star and P. yoelii-GFP) Anti-infective testing including in vitro EC50, in vivo mice infection are available against for major parasitic diseases: Malaria, Leishmaniasis, Chagas and African Trypanosomiasis.

Proper citation: NYU Anti-Infectives Screening and Insectary Core Facilities (RRID:SCR_012350) Copy   

•   Source: SciCrunch Registry

http://www.scienceexchange.com/facilities/gene-targeting-and-transgenic-core-rochester

Currently, the Gene Targeting and Transgenic Core''s services include the production of mouse models using DNA microinjection and embryonic stem cell injection (from gene targeting in mouse ES cells to production of chimeric mice) methodologies. Additional services have included: various analytical techniques, embryo cryopreservation, rederivation of pathogen-free rodents, and assisted reproduction techniques (e.g., in vitro fertilization (IVF), superovulation, and embryo transfer). Specific strains, and alternative species and methods are considered when appropriate for individual research applications.

Proper citation: URMC Gene Targeting and Transgenic Core (RRID:SCR_012367) Copy   

•   Source: SciCrunch Registry

http://www.scienceexchange.com/facilities/transgenic-mouse-shared-resource-columbia

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 22, 2024. Core facility that specializes in the generation and analysis of genetically modified mice, including transgenic and knockout animals, is an essential technology for biomedical research. Our services include: Production of transgenic mice by pronuclear DNA microinjection and embryo transfer. Production of chimeric mice by blastocyst injection of genetically modified ES cells and embryo transfer, which is part of the procedure of producing knockout or knockin mice. Gene targeting, which involves the electroporation of a targeting vector into pluripotent mouse embryonic stem (ES) cells and the selection of gene-targeted clones. Education of investigators and advice on vector and experimental design for experiments using transgenic and knockout mice. Bioimaging: The Animal Imaging Service provides investigators the opportunity for non-invasive detection, localization, and longitudinal monitoring of primary and metastatic cancer cells in vivo, in allograft, zenograft, transgenic and knock-out mouse models. The IVIS Spectrum (Caliper Life Sciences, Hopkinton MA) uses optical imaging technology to detect bioluminescent and fluorescent reporters across the blue to near infrared wavelength region. DNA samples and ES cell lines are injected in the order in which the signed service request forms are received. Currently, the average time from receipt of the service request to injection is approximately 2 weeks. For ES Cell electroporation and expansion, success in gene targeting cannot be guaranteed due to inherent variability in the frequency of targeting different loci, and the possibility of mistakes or mutations in the targeting vector.

Proper citation: Columbia Transgenic Mouse Shared Resource (RRID:SCR_012640) Copy   

•   Source: SciCrunch Registry

http://corefacilities.case.edu/animal.php

A set of core facilities of Case Western Reserve University School of Medicine which allows users to create and analyze in vivo animal models. The various facilities provide animal care, transgenic models, imaging, irradiation, and phenotyping for research concerning such topics as cancer, metabolic processes, and behavior. In vivo animals provided include mice, zebrafish, and rodents.

Proper citation: CWRU In Vivo Animal Facilities (RRID:SCR_014209) Copy   

•   Source: SciCrunch Registry