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http://cleversysinc.com/?csi_products=freezescan-2#blank

Software for detecting the onset and completion of freezing behavior of a rodent. It outputs the freezing behaviors as a sequential list, allowing for further statistical analysis. Freezescan detects freezing behaviors, random intervals, interval freezing, and activity levels. It also detects animal activity during the experiment and can output in quantitative and graphical form.

Proper citation: FreezeScan (RRID:SCR_014495) Copy   

•   Source: SciCrunch Registry

http://zfrhmaps.tch.harvard.edu/cemh/

Research center investigating molecular hematology through mouse and zebrafish models.

Proper citation: Boston Children's Hospital Center of Excellence in Molecular Hematology (RRID:SCR_015348) Copy   

•   Source: SciCrunch Registry

https://www.generecommender.com

Platform for helping science researchers by recommending gene symbol obtained by AI neural proprietary network able to scan millions of papers. Web tool to extract hidden patterns and correlations among genes and diseases from scientific papers.

Proper citation: GeneRecommender (RRID:SCR_022670) Copy   

•   Source: SciCrunch Registry

https://www.sanger.ac.uk/collaboration/sequencing-idd-regions-nod-mouse-genome/

Genetic variations associated with type 1 diabetes identified by sequencing regions of the non-obese diabetic (NOD) mouse genome and comparing them with the same areas of a diabetes-resistant C57BL/6J reference mouse allowing identification of single nucleotide polymorphisms (SNPs) or other genomic variations putatively associated with diabetes in mice. Finished clones from the targeted insulin-dependent diabetes (Idd) candidate regions are displayed in the NOD clone sequence section of the website, where they can be downloaded either as individual clone sequences or larger contigs that make up the accession golden path (AGP). All sequences are publicly available via the International Nucleotide Sequence Database Collaboration. Two NOD mouse BAC libraries were constructed and the BAC ends sequenced. Clones from the DIL NOD BAC library constructed by RIKEN Genomic Sciences Centre (Japan) in conjunction with the Diabetes and Inflammation Laboratory (DIL) (University of Cambridge) from the NOD/MrkTac mouse strain are designated DIL. Clones from the CHORI-29 NOD BAC library constructed by Pieter de Jong (Children's Hospital, Oakland, California, USA) from the NOD/ShiLtJ mouse strain are designated CHORI-29. All NOD mouse BAC end-sequences have been submitted to the International Nucleotide Sequence Database Consortium (INSDC), deposited in the NCBI trace archive. They have generated a clone map from these two libraries by mapping the BAC end-sequences to the latest assembly of the C57BL/6J mouse reference genome sequence. These BAC end-sequence alignments can then be visualized in the Ensembl mouse genome browser where the alignments of both NOD BAC libraries can be accessed through the Distributed Annotation System (DAS). The Mouse Genomes Project has used the Illumina platform to sequence the entire NOD/ShiLtJ genome and this should help to position unaligned BAC end-sequences to novel non-reference regions of the NOD genome. Further information about the BAC end-sequences, such as their alignment, variation data and Ensembl gene coverage, can be obtained from the NOD mouse ftp site.

Proper citation: Sequencing of Idd regions in the NOD mouse genome (RRID:SCR_001483) Copy   

•   Source: SciCrunch Registry

https://github.com/Sethupathy-Lab/miRquant

Software tool for accurate annotation and quantification of microRNAs and their isomiRs from small RNA-sequencing data. Provides information on quality of sequencing data, genome mapping statistics, abundance of other types of small RNAs such as tDRs and yDRs, prevalence of post transcriptional modifications.

Proper citation: miRquant (RRID:SCR_017261) Copy   

•   Source: SciCrunch Registry

https://nyumc.ilab.agilent.com/service_center/4273

Core offers services for researchers who want to apply advanced molecular genetic techniques in rodent models of physiology and disease. Provides expertise in generating novel mutant and transgenic mouse strains using genome engineering in mouse embryos and in embryonic stem cells (ESCs). Available technologies include:Generation of genome-edited mice by embryo pronuclear microinjection of DNA and genome editors (e.g., CRISPR/Cas9, site-specific recombinases) or traditional BAC transgenesis;Generation of genome-edited mice from mouse embryonic stem cells (mESCs) by chimeric blastocyst injection;Generation of genome-edited mice from mESCs by tetraploid blastocyst injection; Generation of mice from induced pluripotent stem cells;Assisted reproductive technologies; Sperm and embryo cryopreservation, storage and import/export;in vitro fertilization (IVF); Embryo rederivation technologies for animal import into barrier vivaria through quarantine.

Proper citation: NYU Langone’s Advanced Rodent Transgenics Laboratory ART-Lab Core Facility (RRID:SCR_017692) Copy   

•   Source: SciCrunch Registry

http://www.med.unc.edu/cgibd/cores/gnotobiotic

Core facility that supports animal model and basic research projects of CGIBD investigators. Investigators use this resource to examine physiologic and pathophysiologic differences in germ-free, gnotobiotic, and specific pathogen free colonized mice of various genetic backgrounds.

Proper citation: University of North Carolina Center for Gastrointestinal Biology and Disease Gnotobiotic Core (RRID:SCR_015615) Copy   

•   Source: SciCrunch Registry

http://www.med.upenn.edu/genetics/tcmf/

Core facility that provides a centralized service to efficiently produce genetically altered mice for basic research, resulting in reduction in effort and cost to participating investigators.

Proper citation: University of Pennsylvania Center for Molecular Studies in Digestive and Liver Diseases Genetically-Modified Mouse Core (RRID:SCR_015622) Copy   

•   Source: SciCrunch Registry

http://neuroexpresso.org/

Database of mouse brain cell type-specific gene expression datasets. NeuroExpresso is able to demonstrate the use of marker genes for acquiring cell type specific information from whole tissue expression.

Proper citation: NeuroExpresso (RRID:SCR_015724) Copy   

•   Source: SciCrunch Registry

https://github.com/scimemia/M-Track

Source code that allows users to simultaneously track the movement of individual paws during spontaneous grooming episodes and walking in multiple freely-behaving mice/rats. This toolbox provides a simple platform to perform trajectory analysis of paw movement.

Proper citation: M-Track (RRID:SCR_015865) Copy   

•   Source: SciCrunch Registry

http://portal.brain-map.org/

Portal provides access to data and web based applications created for benefit of global research community by Allen Institute for Brain Science. Projects to ombine genomics with neuroanatomy by creating gene expression maps for mouse and human brain. Mouse Brain Atlas, Human Brain Atlas, Developing Mouse Brain Atlas, Developing Human Brain Atlas, Mouse Connectivity Atlas, Non-Human Primate Atlas, and Mouse Spinal Cord Atlas and three related projects Glioblastoma, Mouse Diversity, and Sleep data banks, are used to advance various fields of science especially in neurobiological diseases.

Proper citation: Allen Brain Atlas (RRID:SCR_017001) Copy   

•   Source: SciCrunch Registry

http://marrvel.org/

Web tool to search multiple public variant databases simultaneously and provide a unified interface to facilitate the search process. Used for integration of human and model organism genetic resources to facilitate functional annotation of the human genome. Used for analysis of human genes and variants by cross-disciplinary integration of records available in public databases to facilitate clinical diagnosis and basic research.

Proper citation: MARRVEL (RRID:SCR_016871) Copy   

•   Source: SciCrunch Registry

http://www.bx.psu.edu/~giardine/vision/

International project to analyze mouse and human hematopoiesis, and provide a tractable system with clear clinical significance and importance to NIDDK. Collection of information from the flood of epigenomic data on hematopoietic cells as catalogs of validated regulatory modules, quantitative models for gene regulation, and a guide for translation of research insights from mouse to human.

Proper citation: ValIdated Systematic IntegratiON of epigenomic data (RRID:SCR_016921) 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

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://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

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