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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.

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Resource Name Proper Citation Abbreviations Resource Type Description Keywords Resource Relationships Related Condition Funding Defining Citation Availability Website Status Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Synonyms Record Last Update Mentions Count
CRISPRdirect
 
Resource Report
Resource Website
100+ mentions
CRISPRdirect (RRID:SCR_018186) web service, analysis service resource, production service resource, service resource, data access protocol, software resource Software for designing CRISPR/Cas guide RNA with reduced off target sites. Used for rational design of CRISPR/Cas target. Web server for selecting rational CRISPR/Cas targets from input sequence. Server currently incorporates genomic sequences of human, mouse, rat, marmoset, pig, chicken, frog, zebrafish, Ciona, fruit fly, silkworm, Caenorhabditis elegans, Arabidopsis, rice, Sorghum and budding yeast. CRISP/Cas guide RNA, reduced off target site, design of CRISP/Cas target, selecting rational target, sequence, genomic sequence, RNA, bio.tools is listed by: Debian
is listed by: bio.tools
Japan Science and Technology Agency ;
Ministry of Education ;
Culture ;
Sports ;
Science and Technology of Japan
PMID:25414360 Free, Freely available biotools:CRISPRdirect https://bio.tools/CRISPRdirect SCR_018186 2026-02-13 10:58:08 452
Zebrafish Gene Collection
 
Resource Report
Resource Website
1+ mentions
Zebrafish Gene Collection (RRID:SCR_007054) ZGC biomaterial supply resource, material resource Part of zebrafish genome project. ZGC project to produce cDNA libraries, clones and sequences to provide complete set of full-length (open reading frame) sequences and cDNA clones of expressed genes for zebrafish. All ZGC sequences are deposited in GenBank and clones can be purchased from distributors of IMAGE consortium. With conclusion of ZGC project in September 2008, GenBank records of ZGC sequences will be frozen, without further updates. Since definition of what constitutes full-length coding region for some of genes and transcripts for which we have ZGC clones will likely change in future, users planning to order ZGC clones will need to monitor for these changes. Users can make use of genome browsers and gene-specific databases, such as UCSC Genome browser, NCBI's Map Viewer, and Entrez Gene, to view relevant regions of genome (browsers) or gene-related information (Entrez Gene). cdna library, clone, sequence, full-length open reading frame, cdna clone, frozen, fish, gene, genetic, genome, genomic is listed by: One Mind Biospecimen Bank Listing
is related to: One Mind Biospecimen Bank Listing
is related to: NIDDK Information Network (dkNET)
is related to: Mammalian Gene Collection
is related to: GenBank
is related to: ATCC
has parent organization: National Cancer Institute
NIH Blueprint for Neuroscience Research Free, Freely available nif-0000-00567 https://genecollections.nci.nih.gov/ZGC/ SCR_007054 Zebrafish Gene Collection 2026-02-13 10:55:58 1
ZMP
 
Resource Report
Resource Website
10+ mentions
ZMP (RRID:SCR_006161) ZMP biomaterial supply resource, material resource Create knockout alleles in protein coding genes in the zebrafish genome, using a combination of whole exome enrichment and Illumina next generation sequencing, with the aim to cover them all. Each allele created is analyzed for morphological differences and published on the ZMP site. Transcript counting is performed on alleles with a morphological phenotype. Alleles generated are archived and can be requested from this site through the Zebrafish International Resource Center (ZIRC). You may register to receive updates on genes of interest, or browse a complete list, or search by Ensembl ID, gene name or human and mouse orthologue. phenotype, genome, gene, disease model, allele, orthologue, mutant, chromosome, human orthologue, mouse orthologue, mutation, knockout, human, mouse, transcript is listed by: One Mind Biospecimen Bank Listing
is related to: Zebrafish International Resource Center
has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom
Wellcome Trust Sanger Institute; Hinxton; United Kingdom ;
NIH ;
ZF-HEALTH
Free and open nlx_151662 SCR_006161 Zebrafish Mutation Project (ZMP), Zebrafish Mutation Project, ZMP - Zebrafish Mutation Project 2026-02-13 10:55:46 25
CWRU In Vivo Animal Facilities
 
Resource Report
Resource Website
CWRU In Vivo Animal Facilities (RRID:SCR_014209) core facility, access service resource, service resource 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. core facility, in vivo animal model, mouse model, zebrafish model, rat model, is used by: Integrated Animals
has parent organization: Case Western Reserve University; Ohio; USA
Available to the research community SCR_014209 CWRU In Vivo Animal Core Facilities, Case Western Reserve University In Vivo Animal Core Facilities 2026-02-13 10:57:16 0
Boston Children's Hospital Center of Excellence in Molecular Hematology Zebrafish Core
 
Resource Report
Resource Website
Boston Children's Hospital Center of Excellence in Molecular Hematology Zebrafish Core (RRID:SCR_015355) core facility, access service resource, service resource, resource Zebrafish core facility which generates and maintains transgenic and mutant fish lines for hematology research. It also provides expertise and training in model production, study design, and fish production for research. zebrafish model, transgenic fish, mutant fish line is listed by: NIDDK Information Network (dkNET)
has parent organization: Boston Children's Hospital Center of Excellence in Molecular Hematology
is organization facet of: Boston Children's Hospital Center of Excellence in Molecular Hematology
NIDDK U54DK110805 Available to the research community SCR_015355 2026-02-13 10:57:36 0
Boston Children's Hospital Center of Excellence in Molecular Hematology Stem Cell Engineering and Analysis Core
 
Resource Report
Resource Website
Boston Children's Hospital Center of Excellence in Molecular Hematology Stem Cell Engineering and Analysis Core (RRID:SCR_015352) core facility, access service resource, service resource, resource Core facility for basic and translational stem cell research. The core's areas of expertise include human pluripotent stem cell biology, cGMP cell manufacturing, reprogramming, genome editing, genotyping, laboratory automation, chemical screening, and imaging/image analysis. basic stem cell research, translational stem cell research, stem cell core facility is listed by: NIDDK Information Network (dkNET)
has parent organization: Boston Children's Hospital Center of Excellence in Molecular Hematology
is organization facet of: Boston Children's Hospital Center of Excellence in Molecular Hematology
NIDDK U54DK110805 Available to the research community, Fee for service SCR_015352 2026-02-13 10:57:29 0
Pittsburgh Center for Kidney Research Model Organisms
 
Resource Report
Resource Website
Pittsburgh Center for Kidney Research Model Organisms (RRID:SCR_015288) core facility, access service resource, service resource, resource Core that uses the yeast S. cerevisiae and the zebrafish D. rerio to dissect fundamental aspects of kidney development and protein structure and function. renal disease, protein disorders, kidney disease, zebrafish is listed by: NIDDK Information Network (dkNET)
has parent organization: Pittsburgh Center for Kidney Research
is organization facet of: Pittsburgh Center for Kidney Research
NIDDK P30DK079307;
University of Pittsburgh School of Medicine; Pennsylvania; USA ;
Icahn School of Medicine at Mount Sinai; New York; USA
Available to the research community SCR_015288 2026-02-13 10:57:28 0
University of Alabama at Birmingham Nutrition and Obesity Research Center Animal Models Core
 
Resource Report
Resource Website
University of Alabama at Birmingham Nutrition and Obesity Research Center Animal Models Core (RRID:SCR_015466) core facility, access service resource, service resource, resource Core that provides specialized expertise in the use of animal models and instrumentation to facilitate animal research related to nutrition and obesity. obesity animal model, nutrition animal model, animal model service is listed by: NIDDK Information Network (dkNET)
has parent organization: University of Alabama at Birmingham; Alabama; USA
has parent organization: University of Alabama at Birmingham Nutrition and Obesity Research Center
is organization facet of: University of Alabama at Birmingham Nutrition and Obesity Research Center
Obesity NIDDK P30DK056336 Available to the research community, Fee for service SCR_015466 2026-02-13 10:57:38 0
Ensembl
 
Resource Report
Resource Website
10000+ mentions
Ensembl (RRID:SCR_002344) data or information resource, database Collection of genome databases for vertebrates and other eukaryotic species with DNA and protein sequence search capabilities. Used to automatically annotate genome, integrate this annotation with other available biological data and make data publicly available via web. Ensembl tools include BLAST, BLAT, BioMart and the Variant Effect Predictor (VEP) for all supported species. collection, genome, dataset, database, vertebrate, eukaryotic, DNA, protein, sequence, search, automaticly, annotate, data, bio.tools, FASEB list is used by: NIF Data Federation
is used by: Animal QTLdb
is used by: ChannelPedia
is used by: Blueprint Epigenome
is used by: HmtPhenome
lists: Ensembl Covid-19
is listed by: OMICtools
is listed by: Biositemaps
is listed by: re3data.org
is listed by: LabWorm
is listed by: bio.tools
is listed by: Debian
is listed by: SoftCite
is related to: Ensembl Genomes
is related to: GermOnline
is related to: CandiSNPer
is related to: Human Splicing Finder
is related to: NGS-SNP
is related to: Sanger Mouse Resources Portal
is related to: DECIPHER
is related to: Ensembl Genomes
is related to: PeptideAtlas
is related to: AnimalTFDB
is related to: Bgee: dataBase for Gene Expression Evolution
is related to: FlyMine
is related to: Rat Gene Symbol Tracker
is related to: UniParc at the EBI
is related to: go-db-perl
is related to: UniParc
is related to: g:Profiler
is related to: RIKEN integrated database of mammals
is related to: VBASE2
is related to: p300db
is related to: ShinyGO
has parent organization: European Bioinformatics Institute
has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom
is parent organization of: Ensembl Metazoa
is parent organization of: Ensembl Variation
is parent organization of: Pre Ensembl
is parent organization of: Variant Effect Predictor
is parent organization of: Ensembl Bacteria
is parent organization of: Ensembl Plants
is parent organization of: Ensembl Fungi
is parent organization of: Ensembl Protists
is parent organization of: Ensembl Genome Browser
works with: Genotate
works with: CellPhoneDB
works with: Open Regulatory Annotation Database
works with: Database of genes related to Repeat Expansion Diseases
works with: TarBase
Wellcome Trust ;
EMBL ;
European Union ;
FP7 ;
FP6 ;
MRC ;
NHGRI ;
BBSRC
PMID:24316576
PMID:23203987
nif-0000-21145, OMICS_01647, biotools:ensembl, r3d100010228 https://bio.tools/ensembl
https://sources.debian.org/src/ensembl/
https://doi.org/10.17616/R39K5B
SCR_002344 ENSEMBL 2026-02-11 10:56:26 11652
HomeoDB
 
Resource Report
Resource Website
10+ mentions
HomeoDB (RRID:SCR_015492) data or information resource, database 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. homeobox gene, homeobox gene database, gene database has parent organization: Peking University; Beijing; China
has parent organization: University of Oxford; Oxford; United Kingdom
Marie Curie International Incoming Fellowship THIS RESOURCE IS NO LONGER IN SERVICE SCR_015492 2026-02-11 10:59:10 19
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 2026-02-11 11:00:10 82
Target genes of Wnt/beta-catenin signaling
 
Resource Report
Resource Website
10+ mentions
Target genes of Wnt/beta-catenin signaling (RRID:SCR_007022) Target genes of Wnt/beta-catenin signaling data or information resource, data set A list of target genes of Wnt/beta-catenin signaling. Suggestions for additions are welcome. Direct targets are defined as those with Tcf binding sites and demonstrating that these sites are important. target gene, wnt/beta-catenin signaling, wnt, beta-catenin, signaling, gene has parent organization: Stanford University; Stanford; California Colon cancer, Tumor, Adenocarcinoma, Melanoma, Cancer The community can contribute to this resource nlx_156867 SCR_007022 2026-02-11 10:57:28 24
UniProt Chordata protein annotation program
 
Resource Report
Resource Website
UniProt Chordata protein annotation program (RRID:SCR_007071) Chordata protein annotation program data or information resource, data set Data set of manually annotated chordata-specific proteins as well as those that are widely conserved. The program keeps existing human entries up-to-date and broadens the manual annotation to other vertebrate species, especially model organisms, including great apes, cow, mouse, rat, chicken, zebrafish, as well as Xenopus laevis and Xenopus tropicalis. A draft of the complete human proteome is available in UniProtKB/Swiss-Prot and one of the current priorities of the Chordata protein annotation program is to improve the quality of human sequences provided. To this aim, they are updating sequences which show discrepancies with those predicted from the genome sequence. Dubious isoforms, sequences based on experimental artifacts and protein products derived from erroneous gene model predictions are also revisited. This work is in part done in collaboration with the Hinxton Sequence Forum (HSF), which allows active exchange between UniProt, HAVANA, Ensembl and HGNC groups, as well as with RefSeq database. UniProt is a member of the Consensus CDS project and thye are in the process of reviewing their records to support convergence towards a standard set of protein annotation. They also continuously update human entries with functional annotation, including novel structural, post-translational modification, interaction and enzymatic activity data. In order to identify candidates for re-annotation, they use, among others, information extraction tools such as the STRING database. In addition, they regularly add new sequence variants and maintain disease information. Indeed, this annotation program includes the Variation Annotation Program, the goal of which is to annotate all known human genetic diseases and disease-linked protein variants, as well as neutral polymorphisms. chordata, protein, protein annotation, functional annotation, human, non-human vertebrate, xenopus laevis, xenopus tropicalis, zebrafish, protein sequence, protein sequencing, nucleotide sequence, sequence, annotation, sequence variant, disease, proteome, gold standard is related to: Human Proteomics Initiative
is related to: UniProtKB
has parent organization: UniProt
nlx_143879 SCR_007071 2026-02-11 10:57:29 0
Integrated Nervous System Connectivity
 
Resource Report
Resource Website
Integrated Nervous System Connectivity (RRID:SCR_006391) NSC data or information resource, data set A data set of connectivity statements from BAMS, CoCoMac, BrainMaps, Connectome Wiki, the Hippocampal-Parahippocampal Table of Temporal-Lobe.com, and Avian Brain Circuitry Database. The data set lists which brain sites connectivity is to and from, the organism connectivity is mapped in, and journal references. connectivity, nervous system, macaque, brain, bird, data set uses: Avian Brain Circuitry Database
uses: Temporal-Lobe: Hippocampal - Parahippocampal Neuroanatomy of the Rat
uses: Connectome Wiki
uses: BrainMaps.org
uses: CoCoMac
uses: Brain Architecture Management System
uses: BlueBrain Bluima Connectivity
is used by: NIF Data Federation
has parent organization: Integrated
Data are licensed by their respective owners, Use and distribution is subject to the terms of use by the original resource nif-0000-07732 https://legacy.neuinfo.org/mynif/search.php?q=*&t=indexable&list=cover&nif=nlx_154697-8 https://neuinfo.org/mynif/search.php?q=*&t=indexable&list=cover&nif=nlx_154697-8, http://neuinfo.org/nif/nifgwt.html?query=nif-0000-07732, https://www.neuinfo.org/mynif/search.php?q=*&t=indexable&nif=nif-0000-07732-1 SCR_006391 NIF Integrated Nervous System Connectivity View, Neuroscience Information Framework Integrated Nervous System Connectivity, Integrated NSC View, Integrated NSC, NIF NSC, NIF Integrated NSC, Integrated Nervous System Connectivity View, Nervous System Connectivity 2026-02-11 10:57:19 0
Integrated Gene-Disease Interaction
 
Resource Report
Resource Website
Integrated Gene-Disease Interaction (RRID:SCR_006173) data or information resource, database Virtual database currently indexing interaction between genes and diseases from Online Mendelian Inheritance in Man (OMIM) and Comparative Toxicogenomics Database (CTD). gene, phenotype, disease, interaction, integrated, database is used by: NIF Data Federation
is related to: OMIM
is related to: Comparative Toxicogenomics Database (CTD)
has parent organization: Integrated
NIDA ;
NIH Blueprint for Neuroscience Research
Data are licensed by their respective owners, Use and distribution is subject to the Terms of Use by the original resource nlx_151674 https://legacy.neuinfo.org/mynif/search.php?q=*&t=indexable&list=cover&nif=nlx_154697-7 http://neuinfo.org/nif/nifgwt.html?query=nlx_151674, https://www.neuinfo.org/mynif/search.php?q=*&t=indexable&nif=nlx_151674-1, https://neuinfo.org/mynif/search.php?q=*&t=indexable&list=cover&nif=nlx_154697-7 SCR_006173 Gene-Disease Interaction, NIF Integrated Gene-Disease Interaction, Integrated GDI, NIF Integrated Gene-Disease Interaction View, NIF Gene-Disease Interaction, Integrated Gene-Disease Interaction View 2026-02-11 10:57:17 0
BioGPS: The Gene Portal Hub
 
Resource Report
Resource Website
500+ mentions
BioGPS: The Gene Portal Hub (RRID:SCR_006433) BioGPS data or information resource, database An extensible and customizable gene annotation portal that emphasizes community extensibility and user customizability. It is a complete resource for learning about gene and protein function. Community extensibility reflects a belief that any BioGPS user should be able to add new content to BioGPS using the simple plugin interface, completely independently of the core developer team. User customizability recognizes that not all users are interested in the same set of gene annotation data, so the gene report layouts enable each user to define the information that is most relevant to them. Currently, BioGPS supports eight species: Human (Homo sapiens), Mouse (Mus musculus), Rat (Rattus norvegicus), Fruitfly (Drosophila melanogaster), Nematode (Caenorhabditis elegans), Zebrafish (Danio rerio), Thale-cress (Arabidopsis thaliana), Frog (Xenopus tropicalis), and Pig (Sus scrofa). BioGPS presents data in an ortholog-centric format, which allows users to display mouse plugins next to human ones. Our data for defining orthologs comes from NCBI's HomoloGene database. gene, ortholog, plug-in, report, literature, genetics, expression, reagent, protein, pathway, snp, genomics, gene annotation, function, FASEB list is listed by: Biositemaps
is related to: bioDBcore
is related to: aGEM
has parent organization: Scripps Research Institute
Novartis Research Foundation ;
NIGMS R01GM083924
PMID:19919682 Free, The community can contribute to this resource r3d100012402, nif-0000-10168 http://biogps.gnf.org/
https://doi.org/10.17616/R33J20
SCR_006433 2026-02-11 10:57:20 725
Genomicus
 
Resource Report
Resource Website
50+ mentions
Genomicus (RRID:SCR_011791) Genomicus data or information resource, database 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. genome, gene, synteny, browser, FASEB list is listed by: OMICtools PMID:23193262 OMICS_00914 SCR_011791 2026-02-11 10:58:30 52
ECgene: Gene Modeling with Alternative Splicing
 
Resource Report
Resource Website
10+ mentions
ECgene: Gene Modeling with Alternative Splicing (RRID:SCR_007634) ECgene data or information resource, database Database of functional annotation for alternatively spliced genes. It uses a gene-modeling algorithm that combines the genome-based expressed sequence tag (EST) clustering and graph-theoretic transcript assembly procedures. It contains genome, mRNA, and EST sequence data, as well as a genome browser application. Organisms included in the database are human, dog, chicken, fruit fly, mouse, rhesus, rat, worm, and zebrafish. Annotation is provided for the whole transcriptome, not just the alternatively spliced genes. Several viewers and applications are provided that are useful for the analysis of the transcript structure and gene expression. The summary viewer shows the gene summary and the essence of other annotation programs. The genome browser and the transcript viewer are available for comparing the gene structure of splice variants. Changes in the functional domains by alternative splicing can be seen at a glance in the transcript viewer. Two unique ways of analyzing gene expression is also provided. The SAGE tags deduced from the assembled transcripts are used to delineate quantitative expression patterns from SAGE libraries available publicly. The cDNA libraries of EST sequences in each cluster are used to infer qualitative expression patterns. est cluster, genome, alternative splicing, splice, gene, mrna, est, annotation, gene modeling, structure, function, gene expression, transcript, genome browser, differential expression, snp is listed by: OMICtools
is related to: Gene Ontology
has parent organization: Ewha Womans University; Seoul; South Korea
PMID:17132829
PMID:15805497
PMID:15608289
nif-0000-02780, OMICS_01884 http://genome.ewha.ac.kr/ECgene/ SCR_007634 ECgene - Genome Annotation for Alternative Splicing 2026-02-11 10:57:40 12
Disease Genes Conserved Sequence Tags Database
 
Resource Report
Resource Website
Disease Genes Conserved Sequence Tags Database (RRID:SCR_000760) data or information resource, database A database of conserved sequence elements, identified by a systematic genomic sequence comparison between a set of human genes involved in the pathogenesis of genetic disorders and their murine counterparts. Human and mouse genomic sequences were compared by BLASTZ. Sequences longer than 100 and with identity better than 70 were selected as CSTs and imported into the database. CSTs are extensively annotated with respect to exon/intron structure and other biological parameters. CST counterparts in other species were identified by using BLAST to scan genomes from other species, and selecting on the basis of homology and co-linearity. The database can be accessed by gene, chromosomal location, graphic browser, DNA features, and coding regions. database, conserved sequence element, genomic sequence, human gene, pathogenesis, genetic disorder, blastz, cst Telethon Foundation ;
the Associazione Italiana per la Ricerca sul Cancro (AIRC) ;
the Federazione Italiana per la Ricerca sul Cancro (FIRC) ;
the Italian Ministry for Research (MURST) ;
the National Council for Research (CNR) ;
Regione Campania ;
BioGeM
PMID:15608249 THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-21121 SCR_000760 DG CST Database 2026-02-11 10:56:06 0
BodyMap-Xs
 
Resource Report
Resource Website
1+ mentions
BodyMap-Xs (RRID:SCR_001147) BodyMap-Xs data or information resource, database THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. A taxonomical and anatomical database of latest cross species animal EST data, clustered by UniGene and inter connected by Inparanoid. Users can search by Unigene, RefSeq, or Entrez Gene ID, or search for Gene Name or Tissue type. Data is also sortable and viewable based on qualities of normal, Neoplastic, or other. The last data import appears to be from 2008 expressed sequence tag, comparative genomics, anatomy, taxonomy, brain, blood, connective, reproductive, muscular, alimentary, lung, liver, urinary, endocrine, exocrine, embryo, homology, gene expression, ortholog, paralog has parent organization: DNA DataBank of Japan (DDBJ) Neoplasm, Normal Japanese Ministry of Education Culture Sports Science and Technology MEXT ;
New Energy and Industrial Technology Development Organization
PMID:16381946
PMID:11125076
PMID:10592203
THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-02617 http://bodymap.jp/, http://bodymap.ims.u-tokyo.ac.jp/ SCR_001147 BodyMap-Xs: anatomical and taxonomical breakdown of animal EST, BodyMap, BodyMap- human and mouse gene expression database, BodyMap: human and mouse gene expression database, BodyMap-cross species, BodyMap-Xs(cross species) 2026-02-11 10:56:11 1

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