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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
Picky
 
Resource Report
Resource Website
10+ mentions
Picky (RRID:SCR_010963) Picky software resource A software tool for selecting optimal oligonucleotides (oligos) that allows the rapid and efficient determination of gene-specific oligos based on given gene sets, and can be used for large, complex genomes such as human, mouse, or maize. is listed by: OMICtools
has parent organization: Iowa State University; Iowa; USA
NSF DBI0850195 PMID:15180932
PMID:19849862
PMID:20406469
Free, Public, Acknowledgement requested OMICS_00833 SCR_010963 Picky: Optimal Oligonucleotide Design and Analysis 2026-02-14 02:02:07 37
PolyA DB
 
Resource Report
Resource Website
100+ mentions
PolyA DB (RRID:SCR_007867) PolyA_DB data or information resource, database 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. FASEB list has parent organization: University of Medicine and Dentistry of New Jersey; New Jersey; USA SCR_007867 2026-02-14 02:06:32 101
Peptide Sequence Database
 
Resource Report
Resource Website
Peptide Sequence Database (RRID:SCR_005764) PepSeqDB data or information resource, database The Peptide Sequence Database contains putative peptide sequences from human, mouse, rat, and zebrafish. Compressed to eliminate redundancy, these are about 40 fold smaller than a brute force enumeration. Current and old releases are available for download. Each species'' peptide sequence database comprises peptide sequence data from releveant species specific UniGene and IPI clusters, plus all sequences from their consituent EST, mRNA and protein sequence databases, namely RefSeq proteins and mRNAs, UniProt''s SwissProt and TrEMBL, GenBank mRNA, ESTs, and high-throughput cDNAs, HInv-DB, VEGA, EMBL, IPI protein sequences, plus the enumeration of all combinations of UniProt sequence variants, Met loss PTM, and signal peptide cleavages. The README file contains some information about the non amino-acid symbols O (digest site corresponding to a protein N- or C-terminus) and J (no digest sequence join) used in these peptide sequence databases and information about how to configure various search engines to use them. Some search engines handle (very) long sequences badly and in some cases must be patched to use these peptide sequence databases. All search engines supported by the PepArML meta-search engine can (or can be patched to) successfully search these peptide sequence databases. peptide, sequence has parent organization: Edwards Lab nlx_149230 SCR_005764 2026-02-14 02:06:30 0
ARNIE
 
Resource Report
Resource Website
ARNIE (RRID:SCR_000514) ARNIE data or information resource, database THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 1,2023. Database that integrates the extracellular protein interaction network generated in our lab using AVEXIS technology with spatiotemporal expression patterns for all genes in the network. The tool allows users to browse the network by clicking on individual proteins, or by specifying the spatiotemporal parameters. Clicking on connector lines will allow users to compare stage-matched expression patterns for genes encoding interacting proteins. Additionally, users can rapidly search for their genes in the network using the BLAST server provided. network, orthologue, paralogue, gene, orthologue, protein interaction, protein, blast, extracellular, expression profiling, interaction network, ligand, interaction, signaling is listed by: OMICtools
has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom
MRC ;
Wellcome Trust
PMID:20802085 THIS RESOURCE IS NO LONGER IN SERVICE OMICS_01529 SCR_000514 AVEXIS Receptor Network with Integrated Expression 2026-02-14 02:06:00 0
Bgee: dataBase for Gene Expression Evolution
 
Resource Report
Resource Website
50+ mentions
Bgee: dataBase for Gene Expression Evolution (RRID:SCR_002028) Bgee data or information resource, database Database to retrieve and compare gene expression patterns between animal species. Bgee first maps heterogeneous expression data (currently bulk RNA-Seq, scRNA-Seq, Affymetrix, in situ hybridization, and EST data) to anatomy and development of different species. Bgee is based exclusively on curated healthy wild-type expression data (e.g., no gene knock-out, no treatment, no disease), to provide a comparable reference of gene expression. gene expression, scrna-seq, rna-seq, affymetrix, in situ hybridization, expressed sequence tag, cross specie, comparison, homology, anatomy, developmental stage, gene expression pattern, development, genome, function, chordate, fish, transcriptiome, embryo, adult, mirna, protein coding, prenatal, immature, post-embryonic development, alimentary system, cardiovascular system, nervous system, renal system, reproductive system, respiratory system, skeletal system, ortholog, ontology, FASEB list is related to: Gene Expression Omnibus
is related to: NCBI Sequence Read Archive (SRA)
is related to: ArrayExpress
is related to: Zebrafish Information Network (ZFIN)
is related to: Xenbase
is related to: Mouse Genome Informatics (MGI)
is related to: Berkeley Drosophila Genome Project
is related to: UniGene
is related to: Zebrafish Anatomical Ontology
is related to: eVOC
is related to: Adult Mouse Anatomy Ontology
is related to: Xenopus Anatomy Ontology
is related to: Drosophila anatomy and development ontologies
is related to: Ensembl
has parent organization: SIB Swiss Institute of Bioinformatics
has parent organization: University of Lausanne; Lausanne; Switzerland
Free, Freely available nif-0000-11819, r3d100014596 https://doi.org/10.17616/R31NJNR8 SCR_002028 Bgee: dataBase Gene Expression Evolution, dataBase Gene Expression Evolution 2026-02-14 02:06:04 54
Phenoscape Knowledgebase
 
Resource Report
Resource Website
10+ mentions
Phenoscape Knowledgebase (RRID:SCR_002821) Phenoscape Knowledgebase data or information resource, database Knowledgebase that uses ontologies to integrate phenotypic data from genetic studies of zebrafish with evolutionary variable phenotypes from the systematic literature of ostariophysan fishes. Users can explore the data by searching for anatomical terms, taxa, or gene names. The expert system enables the broad scale analysis of phenotypic variation across taxa and the co-analysis of these evolutionarily variable features with the phenotypic mutants of model organisms. The Knowledgebase currently contains 565,158 phenotype statements about 2,527 taxa, sourced from 57 publications, as well as 38,189 phenotype statements about 4,727 genes, retrieved from ZFIN. 2013-01-26. fish, gene, anatomy, model organism, ostariophysan, phenotype, taxis, ontology, anatomy, variation, taxon, genetic, evolution, development, web service, source code uses: Teleost Anatomy Ontology
is related to: Zebrafish Information Network (ZFIN)
is related to: Catalog of Fishes
is related to: FishBase
is related to: AmphibiaWeb
is related to: NCBI Taxonomy
is related to: Catalogue of Life
has parent organization: NESCent - National Evolutionary Synthesis Center
has parent organization: Phenoscape
is parent organization of: Teleost Taxonomy Ontology
NSF DBI-1062404;
NSF DBI-1062542;
NSF EF-0905606;
NSF BDI-0641025;
NSF EF-0423641
PMID:22736877
PMID:20505755
Free, Freely available nif-0000-24925 SCR_002821 2026-02-14 02:06:09 14
miRNAMap
 
Resource Report
Resource Website
100+ mentions
miRNAMap (RRID:SCR_003156) miRNAMap data or information resource, database A database of experimentally verified microRNAs and miRNA target genes in human, mouse, rat, and other metazoan genomes. In addition to known miRNA targets, three computational tools previously developed, such as miRanda, RNAhybrid and TargetScan, were applied for identifying miRNA targets in 3'-UTR of genes. In order to reduce the false positive prediction of miRNA targets, several criteria are supported for filtering the putative miRNA targets. Furthermore, miRNA expression profiles can provide valuable clues for investigating the properties of miRNAs, such tissue specificity and differential expression in cancer/normal cell. Therefore, we performed the Q-PCR experiments for monitoring the expression profiles of 224 human miRNAs in eighteen major normal tissues in human. The cross-reference between the miRNA expression profiles and the expression profiles of its target genes can provide effective viewpoint to understand the regulatory functions of the miRNA. microrna, genome, FASEB list is listed by: OMICtools
has parent organization: National Chiao Tung University; Hsinchu; Taiwan
PMID:18029362
PMID:16381831
THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-03138, OMICS_00408 SCR_003156 2026-02-14 02:06:13 246
Gemma
 
Resource Report
Resource Website
1000+ mentions
Gemma (RRID:SCR_008007) Gemma data or information resource, database 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. chip, microarray, functional genomics, gene expression, coexpression, differential expression, FASEB list is used by: NIF Data Federation
is used by: Integrated Data Annotation
is listed by: Debian
is listed by: SoftCite
is related to: Gene Ontology
is related to: Gene Expression Omnibus
is related to: Phenocarta
has parent organization: University of British Columbia; British Columbia; Canada
is parent organization of: Neurocarta
NIGMS GM076990;
Canadian Foundation for Innovation ;
Michael Smith Foundation for Health Research ;
Canadian Institutes for Health Research
PMID:22782548 Free, Freely available nif-0000-08127, r3d100012747 https://sources.debian.org/src/gemma/
https://doi.org/10.17616/R36R54
https://doi.org/10.17616/R36R54
SCR_008007 2026-02-14 02:06:41 1112
Zebrafish - SCORE Imaging: Specimen in a Corrected Optical Rotational Enclosure
 
Resource Report
Resource Website
10+ mentions
Zebrafish - SCORE Imaging: Specimen in a Corrected Optical Rotational Enclosure (RRID:SCR_001300) SCORE imaging data or information resource, narrative resource Narrative resource describing a visual data analysis and collection approach that takes advantage of the cylindrical nature of the zebrafish allowing for an efficient and effective method for image capture called, Specimen in a Corrected Optical Rotational Enclosure (SCORE) Imaging. To achieve a non-distorted image, zebrafish were placed in a fluorinated ethylene propylene (FEP) tube with a surrounding, optically corrected imaging solution: water. By similarly matching the refractive index of the housing (FEP tubing) to that of the inner liquid and outer liquid (water), distortion was markedly reduced, producing a crisp imagable specimen that is able to be fully rotated 360 degrees. A similar procedure was established for fixed zebrafish embryos using convenient, readily available borosilicate capillaries surrounded by 75% glycerol. The method described could be applied to chemical genetic screening and other, related high-throughput methods within the fish community and among other scientific fields. format, authoring tool, embryo, microscopy, publishing format, image is listed by: FORCE11
has parent organization: Mayo Clinic Minnesota; Minnesota; USA
has parent organization: University of Minnesota Twin Cities; Minnesota; USA
NIGMS GM63904;
NIDA DA14546
PMID:20528262 nif-0000-07749 SCR_001300 Specimen in a Corrected Optical Rotational Enclosure imaging 2026-02-14 02:06:59 11
APPRIS
 
Resource Report
Resource Website
50+ mentions
APPRIS (RRID:SCR_012019) APPRIS data or information resource, database A database that houses annotations of human splice isoforms. It adds reliable protein structural and functional data and information from cross-species conservation. A visual representation of the annotations for each gene allows users to easily identify functional changes brought about by splicing events. In addition to collecting, integrating and analyzing reliable predictions of the effect of splicing events, it also selects a single reference sequence for each gene, termed the principal isoform, based on the annotations of structure, function and conservation for each transcript. isoform, function, annotation, splice, reference sequence, structure, conservation, transcript, FASEB list is listed by: OMICtools
has parent organization: Spanish National Cancer Research Center
PMID:23161672 Free OMICS_01881 SCR_012019 APPRIS - A system for annotating alternative splice isoforms 2026-02-14 02:06:21 85
Wnt homepage
 
Resource Report
Resource Website
10+ mentions
Wnt homepage (RRID:SCR_000662) Wnt homepage data or information resource, topical portal, portal A resource for members of the Wnt community, providing information on progress in the field, maps on signaling pathways, and methods. The page on reagents lists many resources generously made available to and by the Wnt community. Wnt signaling is discussed in many reviews and in a recent book. There are usually several Wnt meetings per year. wnt signaling, wnt, wnt protein, wnt pathway, signaling, pathway, method, protein, reagent, bibliography has parent organization: Stanford University; Stanford; California Cancer THIS RESOURCE IS NO LONGER IN SERVICE nlx_156863 SCR_000662 the Wnt homepage 2026-02-16 09:45:19 13
Cold Spring Harbor Protocols: Collected Resources - Behavioral Assays
 
Resource Report
Resource Website
100+ mentions
Cold Spring Harbor Protocols: Collected Resources - Behavioral Assays (RRID:SCR_001697) CSH Protocols - Behavioral Assays data or information resource, bibliography A bibliography of published Behavioral Assays by Cold Spring Harbor Protocols. Cold Spring Harbor Protocols is an interdisciplinary journal providing a definitive source of research methods in cell, developmental and molecular biology, genetics, bioinformatics, protein science, computational biology, immunology, neuroscience and imaging. Each monthly issue details multiple essential methods - a mix of cutting-edge and well-established techniques. Newly commissioned protocols and unsolicited submissions are supplemented with articles based on Cold Spring Harbor Laboratorys renowned courses and manuals. All protocols are up-to-date and presented in a consistent, easy-to-follow format. genetics, bioinformatics, cell, computational biology, development, imaging, immunology, journal, molecular, neuroscience, protein, research, behavioral assay, behavior, ant, honeybee, learning, courtship, larvae, adult, stress, olfactory, aggression, sleep, movement, locomotor, circadian, feeding has parent organization: Cold Spring Harbor Laboratory Free, Freely Available nif-0000-10198 SCR_001697 Cold Spring Harbor Protocols - Behavioral Assays 2026-02-16 09:45:34 108
BonZeb project
 
Resource Report
Resource Website
BonZeb project (RRID:SCR_021388) data or information resource, project portal, portal Portal provides tools for investigating visuomotor integration specific to high speed kinematic tracking in small model organisms in closed loop experiments. University of Toronto scientists developed suite of Bonsai modules for specifically tracking and analyzing zebrafish movements and integrating these data with closed-loop experiments. BonZeb modules can also be used in an open-loop fashion for collecting, analyzing, and integrating data from multiple sources in real time, or from offline sources for batch processing of pre-recorded data. Tacking and analyzing zebrafish movements, integrating zebrafish movements data with closed loop experiments, zebrafish movements, OpenBehavior is listed by: OpenBehavior
is related to: BonZeb
has parent organization: University of Toronto; Ontario; Canada
Free, Freely available SCR_021388 BonZeb 2026-02-16 09:50:00 0
The WWW Virtual Library: Model Organisms
 
Resource Report
Resource Website
The WWW Virtual Library: Model Organisms (RRID:SCR_007007) data or information resource, topical portal, portal Catalog of internet resources relating to biological model organisms, and is part of the Biosciences area of the Virtual Library project. The main Model Organisms Library discussed in this website are: * E. coli (bacterium) * Yeasts (Saccharomyces cerevisiae, and other species) * Dictyostelium discoideum (slime mold) * Drosophila melanogaster (fruit fly) * Xenopus laevis (African clawed frog) Many aspects of biology are similar in most or all organisms, but it is frequently much easier to study particular aspects in particular organisms - for instance, genetics is easier in small organisms that breed quickly, and very difficult in humans! The most popular model organisms have strong advantages for experimental research, and become even more useful when other scientists have already worked on them, discovering techniques, genes and other useful information. bacterium, cerevisiae, model organism, saccharomyces, s. cerevisiae, slime mold, xenopus, catalog, link aggregator is listed by: 3DVC nif-0000-20953 SCR_007007 VL 2026-02-16 09:46:51 0
Gene Weaver
 
Resource Report
Resource Website
10+ mentions
Gene Weaver (RRID:SCR_003009) storage service resource, data or information resource, production service resource, analysis service resource, database, service resource, data analysis service, data repository Freely accessible phenotype-centered database with integrated analysis and visualization tools. It combines diverse data sets from multiple species and experiment types, and allows data sharing across collaborative groups or to public users. It was conceived of as a tool for the integration of biological functions based on the molecular processes that subserved them. From these data, an empirically derived ontology may one day be inferred. Users have found the system valuable for a wide range of applications in the arena of functional genomic data integration. phenotype, microarray, gene, genome, functional genomics, process, pathway, function, gene set, genomic data integration, analysis, visualization is used by: NIF Data Federation
is used by: Integrated Datasets
is listed by: OMICtools
is related to: Integrated Manually Extracted Annotation
has parent organization: Jackson Laboratory
Integrative Neuroscience Initiative on Alcoholism ;
NIAAA U01 AA13499;
NIAAA U24 AA13513;
NIAAA R01 AA18776
PMID:22080549
PMID:19733230
Free, Freely available r3d100012464, OMICS_02232, nif-0000-00517 http://ontologicaldiscovery.org/
https://doi.org/10.17616/R3248T
SCR_003009 GeneWeaver, GeneWeaver - A system for the integration of functional genomics experiments, Ontological Discovery Environment, GeneWeaver.org 2026-02-17 10:00:07 34
RAVEN
 
Resource Report
Resource Website
100+ mentions
RAVEN (RRID:SCR_001937) RAVEN data or information resource, production service resource, analysis service resource, database, service resource, data analysis service Tool to search for putative regulatory genetic variation in your favorite gene. Single nucleotide polymorphisms (SNPs) (from dbSNP and user defined) are analyzed for overlap with potential transcription factor binding sites (TFBS) and phylogenetic footprinting using UCSC phastCons scores from multiple alignments of 8 vertebrate genomes., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. transcription factor binding site, phylogenetic footprint, regulatory sequence variation, genetic variation, in silico, regulatory sequence, FASEB list uses: Embassy-domsearch
is listed by: OMICtools
has parent organization: University of British Columbia; British Columbia; Canada
PMID:18208319 THIS RESOURCE IS NO LONGER IN SERVICE OMICS_01932 SCR_001937 Regulatory analysis of Variation in Enhancers, RAVEN - Regulatory analysis of Variation in ENhancers 2026-02-17 09:59:48 127
IDEAL - Intrinsically Disordered proteins with Extensive Annotations and Literature
 
Resource Report
Resource Website
10+ mentions
IDEAL - Intrinsically Disordered proteins with Extensive Annotations and Literature (RRID:SCR_006027) IDEAL data or information resource, production service resource, analysis service resource, database, service resource, data analysis service IDEAL, Intrinsically Disordered proteins with Extensive Annotations and Literature, is a collection of knowledge on experimentally verified intrinsically disordered proteins (IDPs) or intrinsically disordered regions (IDRs). IDEAL contains manually curated annotations on IDPs in locations, structures, and functional sites such as protein binding regions and posttranslational modification sites together with references and structural domain assignments. Protean segment One of the unique phenomena seen in IDPs is so-called the coupled folding and binding, where a short flexible segment can bind to its binding partner with forming a specific structure to act as a molecular recognition element. IDEAL explicitly annotates these regions as protean segment (ProS) when unstructured and structured information are both available in the region. Access to the data All the entries are tabulated in the list and individual entries can be retrieved by using the search tool at the upper-right corner in this page. IDEAL also provides the BLAST search, which can find homologs in IDEAL. All the information in IDEAL can be downloaded in the XML file. intrinsically disordered protein, protein, intrinsically disordered region, region, location, structure, functional site, protein binding region, binding region, posttranslational modification site, reference, structural domain assignment, blast, homolog, simian virus 40, epstein-barr virus, human herpesvirus 1, residue, protean segment, bio.tools is listed by: Debian
is listed by: bio.tools
has parent organization: Nagoya University; Nagoya; Japan
Japanese Ministry of Education Culture Sports Science and Technology MEXT PMID:22067451 biotools:ideal, nlx_151427 https://bio.tools/ideal SCR_006027 IDEAL - Intrinsically Disordered proteins with Extensive Annotations Literature, Intrinsically Disordered proteins with Extensive Annotations and Literature 2026-02-17 10:01:03 10
Zebrafish Neurophenome Project Database
 
Resource Report
Resource Website
1+ mentions
Zebrafish Neurophenome Project Database (RRID:SCR_004482) ZNP storage service resource, data or information resource, service resource, data set, data repository Database of neurobehavioral and physiological data of adult zebrafish models, complementing the available repositories for zebrafish genetic information, by providing a dynamic, open-access data repository of comprehensive, curated collection of results from zebrafish neurobehavioral experiments. As of May 2012, it contains over 4,500 experimental results, from over 75 unique physiological and behavioral tests and 330 different drug treatments. ZNP incorporates validated and curated data from work published in this field, to improve the accessibility of current knowledge to researchers interested in using adult zebrafish models. Overall, this program will allow investigators to rapidly review data, to direct their research using these models. Data and protocol submissions are now being accepted. zebrafish, behavior, pharmacology, psychopharmacology, drug, adult zebrafish, phenotype, model, neurobehavior, physiology is listed by: 3DVC
has parent organization: Tulane University School of Medicine; Louisiana; USA
has parent organization: Zebrafish Neuroscience Research Consortium
Tulane University; Louisiana; USA ;
NIDA DA030900-02
PMID:22171801 Open-access, Please cite nlx_143762 http://www.tulane.edu/%E2%88%BCznpindex/search SCR_004482 ZNPdb, Zebrafish Neurophenome Project, ZNP Database, Zebrafish Neurophenome Database 2026-02-17 10:00:32 2
Zebrafish International Resource Center
 
Resource Report
Resource Website
100+ mentions
Zebrafish International Resource Center (RRID:SCR_005065) ZIRC organism supplier, biomaterial supply resource, material resource Center that supplies access to wild-type, mutant, and transgenic zebrafish lines, EST's/cDNAs, antibodies and fish health services. ZIRC Health Services include diagnostic pathology testing for zebrafish and other small laboratory fish species. RIN, Resource Information Network, zebrafish line, expressed sequence tag, cdna, fish, antibody, pathology, research, embryo, adult, RRID Community Authority is used by: Integrated Animals
is listed by: One Mind Biospecimen Bank Listing
is listed by: Resource Information Network
is related to: One Mind Biospecimen Bank Listing
is related to: ZMP
is related to: NIF Data Federation
is related to: Zebrafish Information Network (ZFIN)
is related to: zfishbook
has parent organization: University of Oregon; Oregon; USA
NICHD HD12546;
NCRR RR12546;
W.M. Keck Foundation ;
NIH Office of the Director P40 OD011021
Restricted nif-0000-00242 http://zebrafish.org/home/guide.php SCR_005065 Zebrafish International Resource Center 2026-02-17 10:00:28 445
ZF-screens
 
Resource Report
Resource Website
ZF-screens (RRID:SCR_003910) data or information resource, portal, service resource, organization portal A commercial organization with expertise and multiple departments that focus on both fish physiology and molecular cell biology. ZF-pharma has developed patented technology for the automated in vivo high-throughput screening of pharmaceutical drug candidates against diseases. They seek industrial partners that are interested in obtaining a license for this technology or, alternatively, would prefer to outsource screening of TB drugs to ZF-pharma. NewCatch BV has developed a tool for use in sustainable aquaculture. The tool will first be used for reproduction of the highly valued fish species eel, pikeperch and sole. They seek industrial / aquaculture partners interested in obtaining a license for ZF-implants in other fish species. NewCatch BV carries out fish reproductive research, for instance European eel (Anguilla anguilla), exploring maturation and reproduction. ZF-Genomics offers multiple sequencing services, including mRNAseq and microRNA analysis and de novo and reference genome assemblies. In addition they also offer the bioinformatics services that are needed to make sense of the sequence data. In addition, they perform Next generation sequencing tasks for (inter)national research project partners and for external customers. next generation sequencing, pharmaceutical, in vivo, reproduction, mrnaseq, microrna, maturation, fish physiology, fish molecular cell biology is related to: Predict-TB Commercial nlx_158253 SCR_003910 ZF Screens, ZF-screens BV, ZF-screens B.V. 2026-02-17 10:00:08 0

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