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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
EPIGEN
 
Resource Report
Resource Website
10+ mentions
EPIGEN (RRID:SCR_000093) EPIGEN data or information resource, organization portal, portal, consortium THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16,2023. Group of clinical care and epilepsy research centers who are committed to improving the lives of people with epilepsy through an understanding of the genetics of epilepsy. The consoritum was in an effort to speed discovery to epilepsy genetics by pooling the resources of several research centres., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. epilepsy, genetics, gene, mri, genetic variation, clinical has parent organization: Duke University; North Carolina; USA
has parent organization: University College London; London; United Kingdom
has parent organization: Beaumont Hospital; Dublin; Ireland
has parent organization: Royal College of Surgeons in Ireland; Dublin; Ireland
has parent organization: Free University of Brussels; Brussels; Belgium
Epilepsy THIS RESOURCE IS NO LONGER IN SERVICE nlx_143740 SCR_000093 EPIGEN: An international consortium dedicated to tackling epilepsy through genetics, EPIGEN Consortium 2026-02-14 01:59:36 24
RSEM
 
Resource Report
Resource Website
50+ mentions
RSEM (RRID:SCR_000262) data analysis software, software resource, data processing software, software application Software package for quantifying gene and isoform abundances from single end or paired end RNA Seq data. Accurate transcript quantification from RNA Seq data with or without reference genome. Used for accurate quantification of gene and isoform expression from RNA-Seq data. quantifying, gene, isoform, abundance, single, end, paired, RNA seq, data, transcript, reference, genome, bio.tools is listed by: OMICtools
is listed by: GitHub
is listed by: bio.tools
is listed by: Debian
has parent organization: University of Wisconsin-Madison; Wisconsin; USA
PMID:21816040 Free, Available for download, Freely available OMICS_01966, OMICS_01287, biotools:rsem, SCR_013027 https://github.com/deweylab/RSEM
https://github.com/deweylab/RSEM/releases
https://bio.tools/rsem
https://sources.debian.org/src/rsem/
SCR_000262 RSEM, RNA-Seq by Expectation-Maximization, RSEM-v1.3.0 2026-02-14 01:59:40 94
iFad
 
Resource Report
Resource Website
iFad (RRID:SCR_000271) iFad software resource An R software package implementing a bayesian sparse factor model for the joint analysis of paired datasets, the gene expression and drug sensitivity profiles, measured across the same panel of samples, e.g. cell lines. r, gene expression, drug sensitivity, analysis, drug-pathway association, gene-pathway, pathway, gene, drug is listed by: OMICtools
has parent organization: Yale School of Medicine; Connecticut; USA
PMID:22581178 Free, Available for download, Freely available OMICS_01959 SCR_000271 2026-02-14 01:59:40 0
High-Throughput GoMiner
 
Resource Report
Resource Website
1+ mentions
High-Throughput GoMiner (RRID:SCR_000173) software resource, web application THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A web program that organizes lists of genes of interest (for example, under- and overexpressed genes from a microarray experiment) for biological interpretation in the context of the Gene Ontology and automates the analysis of multiple microarrays then integrates the results across all of them in exportable output files and visualizations. High-Throughput GoMiner is an enhancement of GoMiner and is implemented with both a command line interface and a web interface. The program can also: efficiently perform automated batch processing of an arbitrary number of microarrays; produce a human- or computer-readable report that rank-orders the multiple microarray results according to the number of significant GO categories; integrate the multiple microarray results by providing organized, global clustered image map visualizations of the relationships of significant GO categories; provide a fast form of false discovery rate multiple comparisons calculation; and provide annotations and visualizations for relating transcription factor binding sites to genes and GO categories. term enrichment, gene ontology, gene, microarray, common variable immune deficiency, high-throughput, visualization, database is listed by: Gene Ontology Tools
is related to: Gene Ontology
is related to: GoMiner
has parent organization: National Cancer Institute
has parent organization: National Cancer Institute
NCI 1Z01BC010842-01 PMID:15998470 THIS RESOURCE IS NO LONGER IN SERVICE nlx_149300 SCR_000173 2026-02-14 01:59:38 2
GPViz
 
Resource Report
Resource Website
GPViz (RRID:SCR_000346) GPViz software resource A versatile Java-based software used for dynamic gene-centered visualization of genomic regions and/or variants. gene, visualization, genomic, variant, bioinformatics, java is listed by: OMICtools Free, Available for download, Freely available OMICS_00915 SCR_000346 2026-02-14 01:59:41 0
TEDDY
 
Resource Report
Resource Website
1+ mentions
TEDDY (RRID:SCR_000383) TEDDY clinical trial, portal, consortium, data or information resource, organization portal, database International consortium of six centers assembled to participate in the development and implementation of studies to identify infectious agents, dietary factors, or other environmental agents, including psychosocial factors, that trigger type 1 diabetes in genetically susceptible people. The coordinating centers recruit and enroll subjects, obtaining informed consent from parents prior to or shortly after birth, genetic and other types of samples from neonates and parents, and prospectively following selected neonates throughout childhood or until development of islet autoimmunity or T1DM. The study tracks child diet, illnesses, allergies and other life experiences. A blood sample is taken from children every 3 months for 4 years. After 4 years, children will be seen every 6 months until the age of 15 years. Children are tested for 3 different autoantibodies. The study will compare the life experiences and blood and stool tests of the children who get autoantibodies and diabetes with some of those children who do not get autoantibodies or diabetes. In this way the study hopes to find the triggers of T1DM in children with higher risk genes. consortium, gene, infectious agent, dietary factor, environmental factor, young human, insulin, child, pediatric, autoantibody, blood, stool, biomaterial supply resource, longitudinal, neonate, parent, genetic risk, genetic factor, observation, prospective, serum, plasma, peripheral blood mononuclear cell, saliva, nasal swab, nail clipping, water, dna, virus, nutrition, toxic agent, socioeconomic, psychosocial, male, female, environment, exposure, diet, toxin, infectious agent, bacterial, viral, immunization is listed by: One Mind Biospecimen Bank Listing
is listed by: ClinicalTrials.gov
is listed by: NIDDK Information Network (dkNET)
is listed by: NIDDK Central Repository
is related to: Teddy study IA prediction
has parent organization: University of South Florida; Florida; USA
Type 1 diabetes, Diabetes NIDDK 2UC4DK063829 PMID:21564455 nlx_152857 SCR_000383 The Environmental Determinants of Diabetes in the Young, TEDDY study 2026-02-14 01:59:44 3
ARB project
 
Resource Report
Resource Website
10+ mentions
ARB project (RRID:SCR_000515) ARB software resource Software environment for maintaining databases of molecular sequences and additional information, and for analyzing the sequence data, with emphasis on phylogeny reconstruction. Programs have primarily been developed for ribosomal ribonucleic acid (rRNA) sequences and, therefore, contain special tools for alignment and analysis of these structures. However, other molecular sequence data can also be handled. Protein gene sequences and predicted protein primary structures as well as protein secondary structures can be stored in the same database. ARB package is designed for graphical user interface. Program control and data display are available in a hierarchical set of windows and subwindows. Majority of operations can be controlled using mouse for moving pointer and the left mouse button for initiating and performing operations. rrna sequence, rrna, phylogeny, alignment, analysis, protein, gene is listed by: Debian
is related to: SILVA
is related to: SINA
has parent organization: Technical University of Munich; Bavaria; Germany
PMID:14985472 Free, Available for download, Freely available OMICS_01515 https://sources.debian.org/src/arb/ SCR_000515 The ARB project 2026-02-14 01:59:45 28
RefFinder
 
Resource Report
Resource Website
10+ mentions
RefFinder (RRID:SCR_000472) RefFinder web service, analysis service resource, production service resource, service resource, data access protocol, software resource THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 1,2023. Web-based tool for evaluating and screening reference genes from extensive experimental datasets. It integrates major computational programs (geNorm, Normfinder, BestKeeper, and the comparative delta-Ct method) to compare and rank the tested candidate reference genes. Based on the rankings from each program, it assigns an appropriate weight to an individual gene and calculated the geometric mean of their weights for the overall final ranking., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. gene, gene expression, reference gene, web based tool uses: BestKeeper
uses: NormFinder
uses: geNORM
is listed by: OMICtools
has parent organization: East Carolina University; Carolina; USA
THIS RESOURCE IS NO LONGER IN SERVICE OMICS_02321 http://www.leonxie.com/referencegene.php SCR_000472 2026-02-14 01:59:44 45
GeneCommittee
 
Resource Report
Resource Website
GeneCommittee (RRID:SCR_004168) geneCommittee data analysis service, analysis service resource, production service resource, service resource, software resource Tool for extensively testing the discriminatory power of biologically relevant gene sets in microarray data classification. While the user can work with different gene set collections and several microarray data files to configure specific classification experiments, the tool is able to run several tests in parallel. It is able to render valuable information for diagnostic analyses and clinical management decisions based on systematically evaluating custom hypothesis over different data sets using complementary classifiers, a key aspect in clinical research. dna, microarray, rna-seq, gene expression, classification, gene set, gene, gene set enrichment, functional annotation is listed by: OMICtools
has parent organization: University of Vigo; Galicia; Spain
PMID:24475928 Acknowledgement requested OMICS_02291 https://github.com/michada/GeneCommittee SCR_004168 2026-02-14 02:00:37 0
HLASeq
 
Resource Report
Resource Website
HLASeq (RRID:SCR_004185) HLASeq software resource An open-source software tool for accurate genotyping the human HLA genes from Illumina GA high-throughput sequencing data. genotyping, hla, next generation sequencing, gene, command-line, python is listed by: OMICtools
has parent organization: SourceForge
GNU General Public License, v3 OMICS_01543 SCR_004185 2026-02-14 02:00:38 0
BrainSpan
 
Resource Report
Resource Website
1+ mentions
BrainSpan (RRID:SCR_004219) expression atlas, data or information resource, atlas Atlas of developing human brain for studying transcriptional mechanisms involved in human brain development. One of the BrainSpan datasets, Exon microarray summarized to genes, is presented. It is a downloadable archive of files containing normalized RNA-Seq expression values for analysis. brain, development, brain development, exon, microarray, gene, rna-seq, expression value, expression is used by: NIF Data Federation
has parent organization: Allen Human Brain Atlas: BrainSpan (Atlas of the Developing Brain)
Free, Freely available nlx_98194, nlx_86215, SCR_004877, SCR_005029, SCR_004344, nlx_37081, nlx_2397 http://brainspan.org/rnaseq/downloads.html?format=html
http://brainspan.org/docs.html
http://brainspan.org/docs.html SCR_004219 BrainSpan: RNA-Seq exons, BrainSpan - Exon microarray summarized to genes 2026-02-14 02:00:55 2
TAGS
 
Resource Report
Resource Website
100+ mentions
TAGS (RRID:SCR_004294) TAGS data processing software, data analysis software, time-series analysis software, software application, software resource Software tool for gene set enrichment analysis for expression time series, which can incorporate existing knowledge and analyze the dynamic property of a group of genes that have functional or structural associations. The installation file is for Windows., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. gene, enrichment analysis, time series, function, structure, bio.tools is listed by: bio.tools
is listed by: Debian
has parent organization: Tsinghua University; Beijing; China
THIS RESOURCE IS NO LONGER IN SERVICE biotools:tags, nlx_31187 https://bio.tools/tags http://166.111.130.26/member/yliu/TAGS/ SCR_004294 2026-02-14 02:00:57 139
dkCOIN
 
Resource Report
Resource Website
1+ mentions
dkCOIN (RRID:SCR_004438) dkCOIN data or information resource, database, resource THIS RESOURCE IS NO LONGER IN SERVICE, documented October 13, 2014. The resource has moved to the NIDDKInformation Network (dkNET) project. Contact them at info_at_dknet.org with any questions. Database of large pools of data relevant to the mission of NIDDKwith the goal of developing a community-based network for integration across disciplines to include the larger DKuniverse of diseases, investigators, and potential users. The focus is on greater use of this data with the objective of adding value by breaking down barriers between sites to facilitate linking of different datasets. To date (2013/06/10), a total of 1,195 resources have been associated with one or more genes. Of 11,580 total genes associated with resources, the ten most represented are associated with 359 distinct resources. The main method by which they currently interconnect resources between the providers is via EntrezGene identifiers. A total of 780 unique genes provide the connectivity between 3,159 resource pairs across consortia. To further increase interconnectivity, the groups have been further annotating their data with additional gene identifiers, publications, and ontology terms from selected Open Biological and Biomedical Ontologies (OBO). gene, adenovirus construct, antibody, co-immunoprecipitation, embryonic stem cell line, functional genomics, histology, mouse strain, pcr primer, protocol, real time pcr, metadata, diabetes, stem cell, metabolism, tissue development, web service, cloud, embryonic stem cell is used by: NIF Data Federation
is related to: Beta Cell Biology Consortium
is related to: NIDDK Information Network (dkNET)
is related to: National Mouse Metabolic Phenotyping Centers
is related to: Nuclear Receptor Signaling Atlas
is related to: Diabetic Complications Consortium
is related to: T1DBase
is related to: OBO
has parent organization: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases
NIDDK 3U01DK072473-05S3;
NIDDK 5U24DK076169;
NIDDK U19DK062434
PMID:22734043 THIS RESOURCE IS NO LONGER IN SERVICE nlx_44256 SCR_004438 NIDDKConsortium Interconnectivity Network 2026-02-14 02:00:41 1
NEXTDB
 
Resource Report
Resource Website
10+ mentions
NEXTDB (RRID:SCR_004480) NextDB data analysis service, expression atlas, analysis service resource, data or information resource, production service resource, atlas, service resource, database Expression pattern map of the 100Mb genome of the nematode Caenorhabditis elegans through EST analysis and systematic whole mount in situ hybridization. NEXTDB is the database to integrate all information from their expression pattern project and to make the data available to the scientific community. Information available in the current version is as follows: * Map: Visual expression of the relationships among the cosmids, predicted genes and the cDNA clones. * Image: In situ hybridization images that are arranged by their developmental stages. * Sequence: Tag sequences of the cDNA clones are available. * Homology: Results of BLASTX search are available. Users of the data presented on our web pages should not publish the information without our permission and appropriate acknowledgment. Methods are available for: * In situ hybridization on whole mount embryos of C.elegans * Protocols for large scale in situ hybridization on C.elegans larvae rnai phenotype, homology, blast, fasta, chromosome map, cosmid, gene, cdna clone, genome, in situ hybridization, expressed sequence tag, developmental stage, sequence, embryonic caenorhabditis elegans, chromosome, phenotype, blastx, clone, sequence tag, yac, predicted gene, protein, development, larval caenorhabditis elegans, image collection, experimental protocol, FASEB list is related to: Expression Patterns for C. elegans promoter GFP fusions
is related to: Expression Patterns for C. elegans promoter GFP fusions
has parent organization: National Institute of Genetics; Shizuoka; Japan
Core Research for Evolutional Science and Technology ;
Japan Science and Technology Corporation ;
Japanese Ministry of Education Culture Sports Science and Technology MEXT
Permission required, Acknowledgement required nlx_46406 SCR_004480 Nematode Expression Pattern DataBase 2026-02-14 02:00:41 35
Stem Cell Commons
 
Resource Report
Resource Website
1+ mentions
Stem Cell Commons (RRID:SCR_004415) Stem Cell Commons data repository, storage service resource, analysis service resource, data set, data or information resource, production service resource, source code, service resource, software resource, database Open source environment for sharing, processing and analyzing stem cell data bringing together stem cell data sets with tools for curation, dissemination and analysis. Standardization of the analytical approaches will enable researchers to directly compare and integrate their results with experiments and disease models in the Commons. Key features of the Stem Cell Commons * Contains stem cell related experiments * Includes microarray and Next-Generation Sequencing (NGS) data from human, mouse, rat and zebrafish * Data from multiple cell types and disease models * Carefully curated experimental metadata using controlled vocabularies * Export in the Investigation-Study-Assay tabular format (ISA-Tab) that is used by over 30 organizations worldwide * A community oriented resource with public data sets and freely available code in public code repositories such as GitHub Currently in development * Development of Refinery, a novel analysis platform that links Commons data to the Galaxy analytical engine * ChIP-seq analysis pipeline (additional pipelines in development) * Integration of experimental metadata and data files with Galaxy to guide users to choose workflows, parameters, and data sources Stem Cell Commons is based on open source software and is available for download and development. therapeutic target, blood, stem cell, self-renewal, embryonic stem cell, hematopoietic stem cell, leukemia stem cell, gene, protein, phenotype, therapeutic, annotate, share, analyze, data sharing, statistics, visualize, analyze, microarray, next-generation sequencing, statistics, transcription profiling, genome, genome browser, disease model is related to: Galaxy
is related to: ISA Infrastructure for Managing Experimental Metadata
has parent organization: Harvard Stem Cell Institute
Normal, Acute Myelogenous Leukemia, Glioblastoma, Primitive Neuroectodermal Tumor, Etc. PMID:24303302 Open unspecified license nlx_42085 http://bloodprogram.hsci.harvard.edu/ SCR_004415 HSCI Blood Genomics, Harvard Stem Cell Institute Blood Genomics, Harvard Stem Cell Institute Blood Program, HSCI Blood Program 2026-02-14 02:00:43 2
Handbook of Genetic Counseling
 
Resource Report
Resource Website
Handbook of Genetic Counseling (RRID:SCR_004564) Handbook of Genetic Counseling narrative resource, data or information resource, wiki, book The Handbook of Genetic Counseling is a wikibook designed as an introduction to the discipline and practice of genetic counseling. The text provides an introduction to genetic counseling as a clinical practice and includes sample counseling outlines and letters for students of genetic counseling. Additional outline and letter examples are highly encouraged. Wikibooks contains books on many medical topics; however, no warranty whatsoever is made that any of the books are accurate. gene, counseling, genetic, syndrome, disease has parent organization: Wikibooks nlx_79147 SCR_004564 2026-02-14 02:00:59 0
NCBI BioSystems Database
 
Resource Report
Resource Website
100+ mentions
NCBI BioSystems Database (RRID:SCR_004690) BioSystems data repository, storage service resource, data analysis service, analysis service resource, data or information resource, production service resource, service resource, database Database that provides access to biological systems and their component genes, proteins, and small molecules, as well as literature describing those biosystems and other related data throughout Entrez. A biosystem, or biological system, is a group of molecules that interact directly or indirectly, where the grouping is relevant to the characterization of living matter. BioSystem records list and categorize components, such as the genes, proteins, and small molecules involved in a biological system. The companion FLink tool, in turn, allows you to input a list of proteins, genes, or small molecules and retrieve a ranked list of biosystems. A number of databases provide diagrams showing the components and products of biological pathways along with corresponding annotations and links to literature. This database was developed as a complementary project to (1) serve as a centralized repository of data; (2) connect the biosystem records with associated literature, molecular, and chemical data throughout the Entrez system; and (3) facilitate computation on biosystems data. The NCBI BioSystems Database currently contains records from several source databases: KEGG, BioCyc (including its Tier 1 EcoCyc and MetaCyc databases, and its Tier 2 databases), Reactome, the National Cancer Institute's Pathway Interaction Database, WikiPathways, and Gene Ontology (GO). It includes several types of records such as pathways, structural complexes, and functional sets, and is desiged to accomodate other record types, such as diseases, as data become available. Through these collaborations, the BioSystems database facilitates access to, and provides the ability to compute on, a wide range of biosystems data. If you are interested in depositing data into the BioSystems database, please contact them. pathway, disease, gene, protein, small molecule, literature, computation, image, biomarker, drug, structural complex, functional set, biological system, molecule, gold standard, bio.tools is listed by: re3data.org
is listed by: Debian
is listed by: bio.tools
is related to: KEGG
is related to: NCBI Structure
is related to: BioCyc
is related to: EcoCyc
is related to: MetaCyc
is related to: Reactome
is related to: Pathway Interaction Database
is related to: WikiPathways
is related to: Gene Ontology
has parent organization: NCBI
NIH PMID:19854944 r3d100011033, biotools:biosystems, nlx_69646 https://bio.tools/biosystems
https://doi.org/10.17616/R31K80
SCR_004690 BioSystems Database, NCBI BioSystems 2026-02-14 02:00:59 118
QuickGO
 
Resource Report
Resource Website
500+ mentions
QuickGO (RRID:SCR_004608) QuickGO ontology, web service, data or information resource, controlled vocabulary, data access protocol, software resource, database A web-based browser for Gene Ontology terms and annotations, which is provided by the UniProtKB-GOA group at the EBI. It is able to offer a range of facilities including bulk downloads of GO annotation data which can be extensively filtered by a range of different parameters and GO slim set generation. The software for QuickGO is freely available under the Apache 2 license. QuickGO can supply GO term information and GO annotation data via REST web services. gene, ontology, annotation, browser, visualization, search engine, slimmer-type tool, ontology or annotation browser, ontology or annotation search engine, ontology or annotation visualization, database or data warehouse, windows, mac os x, linux, unix, gold standard, bio.tools is listed by: OMICtools
is listed by: Gene Ontology Tools
is listed by: bio.tools
is listed by: Debian
is related to: Gene Ontology
is related to: STRAP
has parent organization: European Bioinformatics Institute
BBSRC BB/E023541/1 PMID:19744993
PMID:20157483
Apache License, v2, Free for academic use biotools:quickgo, nlx_60318, OMICS_02276 https://bio.tools/quickgo SCR_004608 Quick GO 2026-02-14 02:00:45 523
OpenFlyData.org
 
Resource Report
Resource Website
OpenFlyData.org (RRID:SCR_004807) OpenFlyData.org web service, image collection, data or information resource, data access protocol, software resource, database A cross-database search service for Drosophila gene expression data, including microarray data from FlyAtlas and in situ images from BDGP and Fly-TED. The applications provide different ways to search for and compare gene expression data for the fruit fly Drosophila melanogaster. You may Search Gene Expression Data by Gene, Gene Batch, and by Tissue Expression Profile. A number of Web services (SPARQL endpoints) are provided from this site which may be queried programmatically for data. microarray, in situ, gene expression, gene, open fly data, openflydata, openflydata, expression, in situ hybridization is related to: FlyAtlas: the Drosophila gene expression atlas
is related to: Berkeley Drosophila Genome Project
has parent organization: FlyWeb Project
JISC PMID:20382263 nlx_79461 SCR_004807 open fly data, OpenFlyData, openflydata 2026-02-14 02:01:01 0
Ivy Glioblastoma Atlas Project
 
Resource Report
Resource Website
100+ mentions
Ivy Glioblastoma Atlas Project (RRID:SCR_005044) Ivy GAP data or information resource, image collection, atlas, database Platform for exploring the anatomic and genetic basis of glioblastoma at the cellular and molecular levels that includes two interactive databases linked together by de-identified tumor specimen numbers to facilitate comparisons across data modalities: * The open public image database, here, providing in situ hybridization data mapping gene expression across the anatomic structures inherent in glioblastoma, as well as associated histological data suitable for neuropathological examination * A companion database (Ivy GAP Clinical and Genomic Database) offering detailed clinical, genomic, and expression array data sets that are designed to elucidate the pathways involved in glioblastoma development and progression. This database requires registration for access. The hope is that researchers all over the world will mine these data and identify trends, correlations, and interesting leads for further studies with significant translational and clinical outcomes. The Ivy Glioblastoma Atlas Project is a collaborative partnership between the Ben and Catherine Ivy Foundation, the Allen Institute for Brain Science and the Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment. glioblastoma, in situ hybridization, hematoxylin and eosin stain, brain, tumor, gene expression, anatomic structure, histology, clinical, genomic, expression array, gene, FASEB list has parent organization: Allen Institute for Brain Science Brain cancer, Cancer Ben and Catherine Ivy Foundation nlx_99161 SCR_005044 2026-02-14 02:00:50 126

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