{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,23]],"date-time":"2026-09-23T00:04:45Z","timestamp":1790121885862,"version":"4.0.1"},"reference-count":22,"publisher":"Elsevier BV","issue":"3","license":[{"start":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T00:00:00Z","timestamp":1788220800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T00:00:00Z","timestamp":1788220800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2026,7,28]],"date-time":"2026-07-28T00:00:00Z","timestamp":1785196800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100013105","name":"Shanghai Rising-Star Program","doi-asserted-by":"publisher","award":["23YF1452700"],"award-info":[{"award-number":["23YF1452700"]}],"id":[{"id":"10.13039\/501100013105","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007219","name":"Natural Science Foundation of Shanghai Municipality","doi-asserted-by":"publisher","award":["25ZR1402524"],"award-info":[{"award-number":["25ZR1402524"]}],"id":[{"id":"10.13039\/100007219","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["82271760"],"award-info":[{"award-number":["82271760"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2023YFA0913700"],"award-info":[{"award-number":["2023YFA0913700"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100013102","name":"Shanghai Municipal Youth Science and Technology Star Project","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100013102","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["cell.com","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["STAR Protocols"],"published-print":{"date-parts":[[2026,9]]},"DOI":"10.1016\/j.xpro.2026.104782","type":"journal-article","created":{"date-parts":[[2026,8,13]],"date-time":"2026-08-13T16:06:10Z","timestamp":1786637170000},"page":"104782","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":0,"title":["Protocol for high-throughput genome-wide translocation sequencing-based profiling of T-cell receptor \u03b1 and \u03b2 gene rearrangements in mouse T cells"],"prefix":"10.1016","volume":"7","author":[{"given":"Rui","family":"Luo","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yawei","family":"Song","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dingpeng","family":"Yang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yutong","family":"Xie","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaoling","family":"Qian","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wei","family":"Wu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hai-Qiang","family":"Dai","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.xpro.2026.104782_bib1","article-title":"HTGTS-TCR-Seq for Profiling of Mouse and Human T-Cell Receptor \u03b1 and \u03b2 Gene Rearrangements and Diversity","volume":"13","author":"Luo","year":"2026","journal-title":"Adv. Sci."},{"key":"10.1016\/j.xpro.2026.104782_bib2","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1016\/j.coi.2009.03.009","article-title":"Mechanics of T cell receptor gene rearrangement","volume":"21","author":"Krangel","year":"2009","journal-title":"Curr. Opin. Immunol."},{"key":"10.1016\/j.xpro.2026.104782_bib3","doi-asserted-by":"crossref","first-page":"2157","DOI":"10.1016\/j.celrep.2017.05.045","article-title":"Tcrd Rearrangement Redirects a Processive Tcra Recombination Program to Expand the Tcra Repertoire","volume":"19","author":"Carico","year":"2017","journal-title":"Cell Rep."},{"key":"10.1016\/j.xpro.2026.104782_bib4","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1038\/s41577-022-00679-3","article-title":"The role of chromatin loop extrusion in antibody diversification","volume":"22","author":"Zhang","year":"2022","journal-title":"Nat. Rev. Immunol."},{"key":"10.1016\/j.xpro.2026.104782_bib5","doi-asserted-by":"crossref","first-page":"8081","DOI":"10.1038\/ncomms9081","article-title":"High-resolution analysis of the human T-cell receptor repertoire","volume":"6","author":"Ruggiero","year":"2015","journal-title":"Nat. Commun."},{"key":"10.1016\/j.xpro.2026.104782_bib6","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1007\/978-1-0716-2740-2_16","article-title":"Methods for Study of Mouse T Cell Receptor \u03b1 and \u03b2 Gene Rearrangements","volume":"2580","author":"Dauphars","year":"2023","journal-title":"Methods Mol. Biol."},{"key":"10.1016\/j.xpro.2026.104782_bib7","doi-asserted-by":"crossref","first-page":"236","DOI":"10.1038\/s41587-020-0656-3","article-title":"Benchmarking of T cell receptor repertoire profiling methods reveals large systematic biases","volume":"39","author":"Barennes","year":"2021","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.xpro.2026.104782_bib8","doi-asserted-by":"crossref","first-page":"4099","DOI":"10.1182\/blood-2009-04-217604","article-title":"Comprehensive assessment of T-cell receptor \u03b2-chain diversity in \u03b1\u03b2 T cells","volume":"114","author":"Robins","year":"2009","journal-title":"Blood"},{"key":"10.1016\/j.xpro.2026.104782_bib9","doi-asserted-by":"crossref","first-page":"459","DOI":"10.1534\/genetics.115.176735","article-title":"IMonitor: a robust pipeline for TCR and BCR repertoire analysis","volume":"201","author":"Zhang","year":"2015","journal-title":"Genetics"},{"key":"10.1016\/j.xpro.2026.104782_bib10","doi-asserted-by":"crossref","first-page":"1518","DOI":"10.1073\/pnas.0913939107","article-title":"High throughput sequencing reveals a complex pattern of dynamic interrelationships among human T cell subsets","volume":"107","author":"Wang","year":"2010","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.xpro.2026.104782_bib11","doi-asserted-by":"crossref","first-page":"3099","DOI":"10.4049\/jimmunol.168.6.3099","article-title":"A novel approach to the analysis of specificity, clonality, and frequency of HIV-specific T cell responses reveals a potential mechanism for control of viral escape","volume":"168","author":"Douek","year":"2002","journal-title":"J. Immunol."},{"key":"10.1016\/j.xpro.2026.104782_bib12","doi-asserted-by":"crossref","first-page":"209.5","DOI":"10.4049\/jimmunol.196.Supp.209.5","article-title":"A SMARTer approach to profiling the human T-cell receptor repertoire","volume":"196","author":"Taylor","year":"2016","journal-title":"J. Immunol."},{"key":"10.1016\/j.xpro.2026.104782_bib13","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1007\/978-1-4939-8885-3_2","article-title":"An economical, quantitative, and robust protocol for high-throughput T cell receptor sequencing from tumor or blood","volume":"1884","author":"Uddin","year":"2019","journal-title":"Methods Mol. Biol."},{"key":"10.1016\/j.xpro.2026.104782_bib14","doi-asserted-by":"crossref","first-page":"377","DOI":"10.1038\/nmeth.1315","article-title":"mRNA-seq whole-transcriptome analysis of a single cell","volume":"6","author":"Tang","year":"2009","journal-title":"Nat. Methods"},{"key":"10.1016\/j.xpro.2026.104782_bib15","doi-asserted-by":"crossref","first-page":"1692","DOI":"10.1038\/s41590-019-0544-5","article-title":"TCR sequencing paired with massively parallel 3\u2032 RNA-seq reveals clonotypic T cell signatures","volume":"20","author":"Tu","year":"2019","journal-title":"Nat. Immunol."},{"key":"10.1016\/j.xpro.2026.104782_bib16","doi-asserted-by":"crossref","first-page":"10","DOI":"10.14806\/ej.17.1.200","article-title":"Cutadapt removes adapter sequences from high-throughput sequencing reads","volume":"17","author":"Martin","year":"2011","journal-title":"EMBnet J."},{"key":"10.1016\/j.xpro.2026.104782_bib17","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0163962","article-title":"SeqKit: a cross-platform and ultrafast toolkit for FASTA\/Q file manipulation","volume":"11","author":"Shen","year":"2016","journal-title":"PLoS One"},{"key":"10.1016\/j.xpro.2026.104782_bib18","doi-asserted-by":"crossref","first-page":"1","DOI":"10.2174\/1875036201307010001","article-title":"Comparison of sequencing utility programs","volume":"7","author":"Aronesty","year":"2013","journal-title":"Open Bioinforma. J."},{"key":"10.1016\/j.xpro.2026.104782_bib19","doi-asserted-by":"crossref","first-page":"W34","DOI":"10.1093\/nar\/gkt382","article-title":"IgBLAST: an immunoglobulin variable domain sequence analysis tool","volume":"41","author":"Ye","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.xpro.2026.104782_bib20","doi-asserted-by":"crossref","first-page":"853","DOI":"10.1038\/nprot.2016.043","article-title":"Detecting DNA double-stranded breaks in mammalian genomes by linear amplification\u2013mediated high-throughput genome-wide translocation sequencing","volume":"11","author":"Hu","year":"2016","journal-title":"Nat. Protoc."},{"key":"10.1016\/j.xpro.2026.104782_bib21","doi-asserted-by":"crossref","first-page":"7846","DOI":"10.1073\/pnas.1608649113","article-title":"Highly sensitive and unbiased approach for elucidating antibody repertoires","volume":"113","author":"Lin","year":"2016","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.xpro.2026.104782_bib22","doi-asserted-by":"crossref","first-page":"D413","DOI":"10.1093\/nar\/gku1056","article-title":"IMGT\u00ae, the international ImMunoGeneTics information system\u00ae 25 years on","volume":"43","author":"Lefranc","year":"2015","journal-title":"Nucleic Acids Res."}],"container-title":["STAR Protocols"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2666166726004351?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2666166726004351?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T23:34:26Z","timestamp":1790120066000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S2666166726004351"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9]]},"references-count":22,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2026,9]]}},"alternative-id":["S2666166726004351"],"URL":"https:\/\/doi.org\/10.1016\/j.xpro.2026.104782","relation":{},"ISSN":["2666-1667"],"issn-type":[{"value":"2666-1667","type":"print"}],"subject":[],"published":{"date-parts":[[2026,9]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Protocol for high-throughput genome-wide translocation sequencing-based profiling of T-cell receptor \u03b1 and \u03b2 gene rearrangements in mouse T cells","name":"articletitle","label":"Article Title"},{"value":"STAR Protocols","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.xpro.2026.104782","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2026 The Authors. Published by Elsevier Inc.","name":"copyright","label":"Copyright"}],"article-number":"104782"}}