{"doi":"10.1128/jvi.00181-25","title":"Development of ferret immune repertoire reference resources and single-cell-based high-throughput profiling assays","abstract":"ABSTRACT Domestic ferrets ( Mustela putorius furo ) are important for modeling human respiratory diseases. However, ferret B and T cell receptors have not been completely identified or annotated, limiting immune repertoire studies. Here, we performed long-read transcriptome sequencing of ferret splenocyte and lymph node samples to obtain over 120,000 high-quality full-length immunoglobin (Ig) and T cell receptor (TCR) transcripts. We constructed a complete reference set of the constant regions of ferret Ig and TCR isotypes and chain types. We also systematically annotated germline Ig and TCR variable (V), diversity (D), joining (J), and constant (C) genes on a recent ferret reference genome assembly. We designed new ferret-specific immune repertoire profiling assays by targeting positions in constant regions without allelic diversity across 11 ferret genome assemblies and experimentally validated them using a commercially compatible single-cell-based platform. These improved resources and assays will enable future studies to fully capture ferret immune repertoire diversity. IMPORTANCE Domestic ferrets ( Mustela putorius furo ) are an increasingly common model organism to study human respiratory diseases such as influenza infections. However, researchers lack ferret-specific reagents and resources to study the immune system and immune response in ferrets. In this study, we developed comprehensive ferret immune repertoire reference resources and assays, which will enable more accurate analyses of the ferret immune system in the future.","journal":"Journal of Virology","year":2025,"id":530018,"datarank":0.3058241409458775,"base_score":1.9459101490553132,"endowment":1.9459101490553132,"self_citation_contribution":0.29188652235829704,"citation_network_contribution":0.013937618587580495,"self_endowment_contribution":0.29188652235829704,"citer_contribution":0.013937618587580495,"corpus_percentile":45.60222789510327,"corpus_rank":7033,"citation_count":6,"citer_count":5,"citers_with_citation_signal":1,"citers_with_endowment":1,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.8402,"is_data_producer":true,"deposit_databanks":{"BioProject":["PRJNA939558"],"GEO":["GSE231948"]},"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-01-01","fair_score":62.5,"fair_percentile":81.0149801284011,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1409366,"name":"Kui Yang","orcid":"0000-0002-0045-5561","position":1,"is_corresponding":false},{"id":821478,"name":"Tammy Tollison","orcid":"0000-0002-7193-8456","position":2,"is_corresponding":false},{"id":1409844,"name":"Sujatha Seenu","orcid":null,"position":3,"is_corresponding":false},{"id":1403009,"name":"Nicole Adams","orcid":"0000-0003-2598-5654","position":4,"is_corresponding":false},{"id":1409367,"name":"Guilhem Zeitoun","orcid":"0009-0002-6742-1646","position":5,"is_corresponding":false},{"id":1409368,"name":"Ifigeneia Sideri","orcid":"0000-0001-9986-7904","position":6,"is_corresponding":false},{"id":1409369,"name":"Géraldine Folch","orcid":"0000-0002-5677-5193","position":7,"is_corresponding":false},{"id":228252,"name":"Hayden Brochu","orcid":"0000-0002-7234-3235","position":8,"is_corresponding":false},{"id":821479,"name":"Hsuan Chou","orcid":"0000-0002-8028-225X","position":9,"is_corresponding":false},{"id":1245073,"name":"Sofia Kossida","orcid":"0000-0003-2482-0022","position":10,"is_corresponding":false},{"id":1409370,"name":"Ian A. York","orcid":"0000-0002-3478-3344","position":11,"is_corresponding":false},{"id":228260,"name":"Xinxia Peng","orcid":"0000-0002-0117-3582","position":12,"is_corresponding":false},{"id":822014,"name":"Evan Walsh","orcid":null,"position":0,"is_corresponding":true}],"reference_count":64,"raw_metadata":null,"created_at":"2026-07-19T02:51:01.235017Z","pmid":"40116504","pmcid":"PMC11998538","fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":94.4444,"fair_a":62.5,"fair_i":60.0,"fair_r":33.3333,"fair_zscore":1.1103,"fair_rationale":{"fair_score":62.5,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":94.44,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"All ferret Iso-seq and single-cell RNA-seq data were deposited into NCBI (BioProject accession no. 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[majority verdict 'no' (3/5 passes agreed)]","anchors":["NIH DMS Plan Element 4 (NOT-OD-21-014) — Data Preservation, Access, and Associated Timelines","NSTC Desirable Characteristics (2022), Organizational Infrastructure: 'Retention Policy'","RDA-A2-01M — 'Metadata is guaranteed to remain available after data is no longer available'"],"scored":false,"signal":null}]},"I":{"name":"Interoperable","score":60.0,"criteria":[{"key":"i_open_nonproprietary_format","label":"Open file format","kind":"llm","weight":1.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No file format (open or proprietary) is named for the released data.","anchors":["FsF-R1.3-02D — F-UJI: 'Data is available in a file format recommended by the target research co","RDA-R1.3-02D — data is expressed in a machine-understandable community standard","RDA-I1-01D — data uses a knowledge representation expressed in a standardised format"],"scored":true,"signal":null},{"key":"i_community_standard_vocabulary","label":"Community standard / vocabulary","kind":"llm","weight":1.0,"fraction":1.0,"verdict":"yes","evidence":"All ferret C, V, D, and J sequences are available in the IMGT database under accession numbers","grounded":true,"rationale":"IMGT is a community-standard database and nomenclature for immunogenetics, registered in FAIRsharing.","anchors":["RDA-R1.3-01M — 'Metadata complies with a community standard' (priority Essential)","RDA-R1.3-01D — 'Data complies with a community standard'","RDA-I2-01M — '(Meta)data use vocabularies that follow FAIR principles'"],"scored":false,"signal":null},{"key":"i_qualified_references","label":"Identifiers for the resources the data depend on","kind":"llm","weight":0.5,"fraction":1.0,"verdict":"yes","evidence":"a recent ferret reference genome assembly (NCBI accession no. 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[majority verdict 'no' (3/5 passes agreed)]","gain":0.0,"priority":"useful","scored":false}],"suggestions":["Attach a standard, machine-readable open licence to the deposit — CC0 or CC BY, which is what Horizon Europe and most funders expect — and print the licence identifier in the paper. 'Free to use' is not a licence: it grants nothing a reuser's institution can rely on.","Release the data in an open, community-standard format (CSV/TSV, JSON, HDF5, NetCDF, FASTQ, VCF, NIfTI…) instead of — or alongside — any proprietary or instrument-native format, and name the format in the paper. A dataset that needs a €2,000 licence to open is not reusable. Prefer open proteomics formats such as mzML or mzIdentML.","Cite the dataset in the reference list like a publication — creator, year, title, repository, DOI/accession — and cite it in-text where it is used. Only a reference- list entry is machine-readable to Crossref/DataCite, and only a citation lets the data earn credit. 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