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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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University of Iowa Center for Gene Therapy Animal Model Core Resource Report Resource Website |
University of Iowa Center for Gene Therapy Animal Model Core (RRID:SCR_015413) | access service resource, resource, service resource, core facility | Core that provides support to investigators who use animal models to study the pathogenesis of cystic fibrosis and who develop gene and other molecular therapies for cystic fibrosis. Specifically, it provides centralized production, care, breeding, genotyping, and quality control of cystic fibrosis mouse and ferret models used by investigators in the Center. | cystic fibrosis animal model, cystic fibrosis pathogenesis, cystic fibrosis gene therapy |
has parent organization: University of Iowa Carver College of Medicine; Iowa; USA has parent organization: University of Iowa Center for Gene Therapy is organization facet of: University of Iowa Center for Gene Therapy |
Cystic Fibrosis | NIDDK P30DK054759 | Available to the research community | SCR_015413 | 2026-08-05 10:46:22 | 0 | ||||||||
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MMPC-University of Michigan Medical School Microbiome Core Resource Report Resource Website |
MMPC-University of Michigan Medical School Microbiome Core (RRID:SCR_015378) | access service resource, service resource, core facility | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 16,2025. Core whose mission is to provide analytical tools to investigators to permit determination of the structure of the microbiome in mouse models of disease and assistance in the cultivation of microbes that will permit hypothesis testing in murine models including the germfree animals that are available in the Animal Care Core. | microbiome, mouse models of disease, murine models, microbes |
is listed by: NIDDK Information Network (dkNET) has parent organization: National Mouse Metabolic Phenotyping Centers has parent organization: University of Michigan; Ann Arbor; USA has parent organization: MMPC-University of Michigan Medical School is organization facet of: MMPC-University of Michigan Medical School |
NIDDK U2C-DK110768 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_015378 | 2026-08-05 10:46:22 | 0 | |||||||||
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University of Iowa Center for Gene Therapy Comparative Pathology Core Resource Report Resource Website |
University of Iowa Center for Gene Therapy Comparative Pathology Core (RRID:SCR_015411) | access service resource, resource, service resource, core facility | Core facility which provides comprehensive necropsy, histology, and pathology services for animal models in order to facilitate translational research in animal models of cystic fibrosis. It also houses instrumentation which allows for high-throughput optimization of immunostaining protocols and has access to morphologic equipment that allow for the scanning of large tissue areas and morphometric quantification of histologic endpoints. | cytstic fibrosis animal model, translational cytstic fibrosis research |
is listed by: NIDDK Information Network (dkNET) has parent organization: University of Iowa Carver College of Medicine; Iowa; USA has parent organization: University of Iowa Center for Gene Therapy is organization facet of: University of Iowa Center for Gene Therapy |
Cystic Fibrosis | NIDDK P30DK054759 | Available to the research community | SCR_015411 | 2026-08-05 10:46:23 | 0 | ||||||||
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MMPC-Vanderbilt University School of Medicine Analytical Resources Core Resource Report Resource Website |
MMPC-Vanderbilt University School of Medicine Analytical Resources Core (RRID:SCR_015379) | access service resource, resource, service resource, core facility | Core that consists of three subcores: Hormone Assay and Analytical Services, Lipids, Lipoproteins, and Atherosclerosis, and Mouse Pathology. The Hormone Assay and Analytical Services provides analyses that facilitate research in diabetic, cardiovascular, and obese animal models. Lipids and Lipoproteins Subcore provides quantitative and qualitative measurements of plasma and tissue lipids and lipoproteins to researchers who use mice to study atherosclerosis, dyslipidemia, diabetes, obesity, hypertension, and other metabolic diseases. Mouse Pathology services include standard pathology testing in hematology, clinical chemistry, parasitology, microbiology, serology, molecular diagnostics, necropsy, and research histology and pathology expertise and counseling. | hormone assay service, hormone analysis service, lipid service, mouse pathology service |
is listed by: NIDDK Information Network (dkNET) has parent organization: National Mouse Metabolic Phenotyping Centers has parent organization: MMPC-Vanderbilt University School of Medicine is organization facet of: MMPC-Vanderbilt University School of Medicine |
NIDDK U24 DK059637 | Available to the research community, Fee for service | SCR_015379 | 2026-08-05 10:46:21 | 0 | |||||||||
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MMPC-University of Cincinnati Medical Center Energy Metabolism Food Intake and Body Weight Regulation Core Resource Report Resource Website |
MMPC-University of Cincinnati Medical Center Energy Metabolism Food Intake and Body Weight Regulation Core (RRID:SCR_015371) | access service resource, resource, service resource, core facility | Core that specializes in total body/carcass analysis, measurement of oxygen consumption and carbon dioxide production, meal pattern analysis, and feeding mass/bouts, drinking volume, VO2 and VCO2. | energy metabolism, energy balance services, food intake, body weight regulation |
is listed by: NIDDK Information Network (dkNET) has parent organization: University of Cincinnati; Ohio; USA has parent organization: National Mouse Metabolic Phenotyping Centers has parent organization: MMPC-University of Cincinnati Medical Center is organization facet of: MMPC-University of Cincinnati Medical Center |
NIDDK DK059630 | Available to the research community | SCR_015371 | 2026-08-05 10:46:22 | 0 | |||||||||
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University of Michigan Center for Gastrointestinal Research Microbiome and Metabolomics Core Resource Report Resource Website |
University of Michigan Center for Gastrointestinal Research Microbiome and Metabolomics Core (RRID:SCR_015611) | UMCGR, MMC, | access service resource, service resource, core facility | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 8,2025. Core whose services include consultation, Nucleic Acid Isolation, Microbiome (16S) Data Analysis, MiSeq-base 16S rRNA Gene Sequencing, Genomic/Metagenomic shotgun sequencing, Bacterial transcriptomics and metatranscriptomics, Multiplatform Metabolomic Profiling, Metabolomic sample preparation, and Germ-free & Gnotobiotic Mouse Facilities. | microbiome, metabolomics, bioinformatics, |
is listed by: NIDDK Information Network (dkNET) has parent organization: University of Michigan Center for Gastrointestinal Research is organization facet of: University of Michigan Center for Gastrointestinal Research |
digestive disease | NIDDK P30 DK034933 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_015611 | Center for Gastrointestinal Research, University of Michigan, Metabolomics Core, Microbiome | 2026-08-05 10:46:26 | 0 | ||||||
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CATlas Resource Report Resource Website 1+ mentions |
CATlas (RRID:SCR_018690) | data or information resource, atlas | 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. | Gene, regulatory element, gene regulatory element, adult mouse, cerebrum, Cis-element, chromatin, mouse isocortex, olfactory bulb, hippocampus, cerebral nuclei, cis regulatory DNA element, brain, neurological disease |
is used by: BICCN is related to: BRAIN Initiative Cell Atlas Network |
DOI:10.1101/2020.05.10.087585 | Free, Freely available | SCR_018690 | , Cis-element Atlas, Ren lab web portal for chromatin accessibility data | 2026-08-05 10:47:05 | 3 | ||||||||
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Allen Institute Mouse Whole Cortex and Hippocampus SMART-seq Resource Report Resource Website 10+ mentions |
Allen Institute Mouse Whole Cortex and Hippocampus SMART-seq (RRID:SCR_019013) | data or information resource, spatially referenced dataset, atlas | 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. | Data collection, single cell transcriptomes, multiple cortical area, hippocampal formation, eight week old mice brain sample, pan GABAergic line, pan glutamatergic line, pan neuronal transgenic line |
has parent organization: Allen Institute for Brain Science is hosted by: Allen Cell Types Database |
Free, Freely available | SCR_019013 | Mouse Whole Cortex and Hippocampus SMART-seq | 2026-08-05 10:47:08 | 16 | |||||||||
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Attie Lab Diabetes Database Resource Report Resource Website 1+ mentions |
Attie Lab Diabetes Database (RRID:SCR_016639) | data or information resource, database | 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. | interactive, database, gene, expression, diabetes, related, clinical, phenotype, mouse |
is listed by: OMICtools has parent organization: University of Wisconsin-Madison; Wisconsin; USA |
diabetes | Free, Freely available | SCR_016639 | 2026-08-05 10:46:42 | 3 | |||||||||
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mousebrain.org Resource Report Resource Website 100+ mentions |
mousebrain.org (RRID:SCR_016999) | data or information resource, atlas | 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. | Atlas, brain cell, cell type, single cell RNA seq data, taxon, tissue, gene, marker, anatomical location, data | has parent organization: Karolinska Institute; Stockholm; Sweden | Knut and Alice Wallenberg Foundation ; Swedish Foundation for Strategic Research ; Wellcome Trust ; Swedish Research Council ; SSF ; Cancerfonden ; EU ; Hjärnfonden ; SFO Strat Regen ; European Research Council ; Ollie and Elof Ericssons Foundation ; Åke Wiberg Foundation |
PMID:30096314 | Free, Available for download, Freely available | SCR_018356 | SCR_016999 | Linnarsson lab Mouse Brain Atlas | 2026-08-05 10:46:47 | 111 | ||||||
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Dfam Resource Report Resource Website 50+ mentions |
Dfam (RRID:SCR_021168) | data or information resource, database | 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. | Transposable Element, DNA sequence alignments, hidden Markov Models, consensus sequences, genome annotations | is related to: RepeatModeler | NHGRI U24 HG010136; NHGRI R01 HG002939 |
DOI:10.1186/s13100-020-00230-y | Free, Freely available | SCR_021168 | Dfam 3.2 | 2026-08-05 10:47:22 | 82 | |||||||
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Resource Identification Portal Resource Report Resource Website 10+ mentions |
Resource Identification Portal (RRID:SCR_004098) | RII Portal | data or information resource, portal | 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. | antibody, organism, service resource, software resource, database, resource, identifier, citation, biomedical, publication, research resource identifier, rrid, ASWG |
uses: Antibody Registry uses: SciCrunch Registry uses: Mouse Genome Informatics (MGI) uses: Zebrafish Information Network (ZFIN) uses: Rat Genome Database (RGD) uses: WormBase uses: FlyBase recommends: SciCrunch Registry recommends: Mouse Genome Informatics (MGI) recommends: Zebrafish Information Network (ZFIN) recommends: Rat Genome Database (RGD) is recommended by: Neuroscience Information Framework is recommended by: SciCrunch Registry is related to: NIF Data Federation has parent organization: SciCrunch |
NIGMS R24 GM144308 | The community can contribute to this resource | nlx_158572 | SCR_004098 | Resource Identification Initiative Portal | 2026-08-05 10:43:58 | 19 | ||||||
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Vanderbilt Diabetes Research and Training Center Islet Procurement and Analysis Core Resource Report Resource Website |
Vanderbilt Diabetes Research and Training Center Islet Procurement and Analysis Core (RRID:SCR_000896) | VU IPA Core | access service resource, resource, service resource, core facility | 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. | diabetes, pancreas, islet functional analysis, pancreatic islet morphology |
is listed by: Eagle I is listed by: NIDDK Information Network (dkNET) has parent organization: Vanderbilt University; Tennessee; USA has parent organization: Vanderbilt Diabetes Research and Training Center is organization facet of: Vanderbilt Diabetes Research and Training Center |
Diabetes | NIDDK DK020593 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156666 | http://eagle-i.ea.vanderbilt.edu/i/00000139-b6a3-c300-b341-4bb480000000 | SCR_000896 | 2026-08-05 10:43:16 | 0 | |||||
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RPCI Gene Targeting and Transgenic Shared Resource Resource Report Resource Website |
RPCI Gene Targeting and Transgenic Shared Resource (RRID:SCR_001020) | access service resource, service resource, core facility | Facility which provides researchers with transgenic mouse technologies, methods, and animal models. Knockout mice, transgenic mice, and mice on multiple strain backgrounds are provided. | core facility, mouse, animal model, transgenic, knockout, cancer, shared resource |
is listed by: ScienceExchange has parent organization: Roswell Park Comprehensive Cancer Center |
NCI P30CA16056 | THIS RESOURCE IS NO LONGER IN SERVICE | SciEx_10094 | http://www.scienceexchange.com/facilities/gene-targeting-and-transgenic-facility | SCR_001020 | RPCI Gene Targeting and Transgenic Facility, Roswell Park Cancer Institute Gene Targeting and Transgenic Facility, Roswell Park Cancer Institute Gene Targeting and Transgenic Shared Resource | 2026-08-05 10:43:17 | 0 | ||||||
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CAGE Basic Viewer for Mus musculus Resource Report Resource Website 1+ mentions |
CAGE Basic Viewer for Mus musculus (RRID:SCR_000451) | CAGE Basic Viewer | data or information resource, data set | A web system, which could search and display to current CAGE library information in CAGE Database. | genome, gene, tissue, library, map, clone, cage, tag, mus musculus, primer, cdna, transcription, mouse development, theiler stage |
is related to: Functional Annotation of the Mammalian Genome is related to: CAGE has parent organization: RIKEN |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30231 | SCR_000451 | 2026-08-05 10:43:10 | 1 | ||||||||
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Perlegen/NIEHS National Toxicology: Mouse Genome Resequencing Project Resource Report Resource Website 1+ mentions |
Perlegen/NIEHS National Toxicology: Mouse Genome Resequencing Project (RRID:SCR_000726) | Mouse Resequencing Project | data or information resource, data set | THIS RESOURCE IS NO LONGER IN SERVICE, Documented on August 12, 2014. Data, grouped by chromosome, available as flat files for download, of identified DNA polymorphisms (SNPs) in 15 commonly used strains of inbred laboratory mice. Perlegen's SNP, genotype (empirical and imputed), haplotype, trace, and PCR primer data has been compiled with NCBI Mouse Build information to produce data files for public use. Using high-density oligonuclueotide array technology, the study identified over 8 million SNPs and other genetic differences between these strains and the previously sequenced C57BL/6J reference strains (Phase 1). By leveraging data provided by Mark Daly's research team at the Broad Institute, genotypes were also predicted for 40 other common strains (Phase 2). Under an extension to the contract, Eleazar Eskin's group at UCLA has used this data to evaluate SNP associations with phenotypes from the Mouse Phenome Project (the Mouse Phenome Database), and to construct haplotype maps for a total of 94 inbred strains (the Mouse HapMap Project). SNP and genotype positions have been mapped from their original reference coordinates to NCBI Mouse Build 37 coordinates. Note that C57BL6/J strain was not selected for re-sequencing as this data would have been almost entirely redundant with the NCBI reference sequence. Since we did not actually determine genotypes for C57BL6/J, we did not submit genotypes for this strain to dbSNP. However, implicit genotypes for C57BL6/J can be obtained from the reference sequence at each SNP position (the reference allele is the first allele in the ALLELES column). The data is available for download in two different compressed file formats. The files are saved as both PC .zip files and Unix compressed .gz files. At this website, you can: * Learn more about the goals of the Perlegen mouse resequencing project. * Learn more about the array-based resequencing technology used in the project. * Download the SNPs, genotypes, and other data generated by the project, plus sequences of the long-range PCR primers used for SNP discovery. * Browse the mouse genome for SNPs. * View the haplotype blocks within the mouse genome. Mouse Genome Browser The Mouse Genome Browser can be used to visualize genes and the SNPs discovered in this study of genome-wide DNA variation in 15 commonly used, genetically diverse strains of inbred laboratory mice. The reference genome is the C57BL/6J strain NCBI build 37 mouse sequence. In addition to the experimentally-derived genotypes for the original 15 strains, the imputed genotypes for 40 additional inbred mouse strains can also be accessed. Mouse Haplotype Analysis The sequences of 16 commonly used, genetically diverse strains of inbred laboratory mice were analyzed to determine their haplotype structure. The Ancestry Browser shows which ancestral sequence each inbred strain most resembles, along with statistics on the pairwise similarity between the ancestral strains. The Haplotype Viewer shows the haplotype block boundaries and the pairwise similarity for all 56 strains: the 15 used for SNP discovery, the reference strain (C57BL/6J), and the 40 additional strains for which the genotypes were imputed. | genetic variation, chromosome, dna, genome, genotype, haplotype, oligonuclueotide, inbred mouse strain, polymorphism, sequence, single-nucleotide polymorphism, c57bl6/j | is related to: Mouse HapMap Imputation Genotype Resource | NIEHS ; HHSN29120045530C (N01-ES-45530) |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21746 | SCR_000726 | 2026-08-05 10:43:13 | 3 | |||||||
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PITA Resource Report Resource Website 1000+ mentions |
PITA (RRID:SCR_010853) | PITA | data or information resource, data set | Catalogs of predicted microRNA targets in worm (based on ce6 genome assembly), fly (dm3), mouse (mm9) and human (hg18). We follow standard seed parameter settings and consider seeds of length 6-8 bases, beginning at position 2 of the microRNA. No mismatches or loops are allowed, but a single G:U wobble is allowed in 7- or 8-mers. In genes missing a 3' UTR annotation, 500 bp (fly), 800 bp (human and mouse) or 300 bp (worm) downstream of the annotated end of the coding sequence were used as the predicted UTR. For each organism, a catalog with zero flank and with a flank of 3 and 15 bases upstream and downstream. | is listed by: OMICtools | OMICS_00412 | SCR_010853 | 2026-08-05 10:45:28 | 1047 | ||||||||||
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Retinal wave repository Resource Report Resource Website |
Retinal wave repository (RRID:SCR_010462) | Retinal wave repository | data or information resource, data set | A subset of the CARMEN repository, a curated set of data and code of multielectrode array recordings of spontaneous activity in developing mouse and ferret retina. The data have been annotated with minimal metadata and converted into HDF5 (Hierarchical data format, version 5) including the essential features of the recordings, such as developmental age, and genotype. All code and tools used in the analyses are also fully available for reuse, giving the ability to regenerate each figure and table and know exactly how the results were calculated, adding confidence in the research output and allowing others to easily build upon previous work. The addition of published data to the repository is encouraged. | hdf5, development, neural circuit, retina, eye, multielectrode, array recording, spontaneous activity, reproducible research, retinal wave, electrophysiology, multielectrode array, developmental age, genotype |
has parent organization: GigaScience has parent organization: Code Analysis Repository and Modelling for e-Neuroscience has parent organization: University of Cambridge; Cambridge; United Kingdom |
Developing retina, Aging | EPSRC EP/E002331/1; BBSRC BB/H023577/1; BBSRC BB/I000984/1; Wellcome Trust 083205/B/07/Z |
PMID:24666584 | Registration required, (CARMEN), Acknowledgement required, The community can contribute to this resource | nlx_157664 | http://www.damtp.cam.ac.uk/user/eglen/waverepo/ | SCR_010462 | A data repository and analysis framework for spontaneous neural activity recordings in developing retina | 2026-08-05 10:45:24 | 0 |
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