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","fileAccessRequest":false,"metadataBlocks":{"citation":{"displayName":"Citation Metadata","name":"citation","fields":[{"typeName":"title","multiple":false,"typeClass":"primitive","value":"Replication Data for: \"Single-cell T-cell Receptor sequencing of paired human atherosclerotic plaques and blood reveals autoimmune-like features of expanded effector T-cells.\""},{"typeName":"author","multiple":true,"typeClass":"compound","value":[{"authorName":{"typeName":"authorName","multiple":false,"typeClass":"primitive","value":"Sander W. van der Laan"},"authorAffiliation":{"typeName":"authorAffiliation","multiple":false,"typeClass":"primitive","value":"UMC Utrecht"},"authorIdentifierScheme":{"typeName":"authorIdentifierScheme","multiple":false,"typeClass":"controlledVocabulary","value":"ORCID"},"authorIdentifier":{"typeName":"authorIdentifier","multiple":false,"typeClass":"primitive","value":"0000-0001-6888-1404"}},{"authorName":{"typeName":"authorName","multiple":false,"typeClass":"primitive","value":"Marie A.C. 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\n
\nAbstract\nWe applied single-cell TCR sequencing (scTCRseq) on human carotid artery plaques and patient matched PBMC samples to assess the extent of TCR clonality and antigen specific activation within the various T-cell subsets on 3 patients, and applied bulk CDR3b sequencing of matched PBMC and plaque material of 10 patients. CellChat was used to analyze potential interactions of effector CD4+ T-cells with foam cells in the plaque. Finally, we integrated a published scTCRseq dataset of the autoimmune disease psoriatic arthritis to assess commonalities and differences between the two diseases. In this repository we provide the raw atherosclerosis TCRseq data, the bulk sequencing data, and the code that was used for the analysis of the data. \n\nGitHub\nA link to the public GitHub repository: link. This contains all scripts used for the data, which is pseudonymized and shared here. \n\n\nAthero-Express Biobank Study\nThe AE started in 2002 and now includes over 3,500 patients who underwent surgery to remove atherosclerotic plaques (endarterectomy) from one (or more) of their major arteries (majority carotids and femorals); this is further described here. The study design and staining protocols are described by Verhoeven et al.\n\nAdditional data\nAdditional clinical data is available upon discussion and signing a Data Sharing Agreement (see Terms of Access).\n\nPlaqView\nPlease note, that we will also integrate these data through PlaqView, but they are not available yet.
In collaboration with the http://millerlab.org from the University of Virginia (USA) we created PlaqView.com. You can query any gene of interest in many carotid-plaque datasets, including ours. From our experience we know that usually this suffices most research questions and prevents the lengthy process of obtaining these data through a DSA."},"dsDescriptionDate":{"typeName":"dsDescriptionDate","multiple":false,"typeClass":"primitive","value":"2022-11-09"}}]},{"typeName":"subject","multiple":true,"typeClass":"controlledVocabulary","value":["Medicine, Health and Life Sciences"]},{"typeName":"keyword","multiple":true,"typeClass":"compound","value":[{"keywordValue":{"typeName":"keywordValue","multiple":false,"typeClass":"primitive","value":"atherosclerosis"}},{"keywordValue":{"typeName":"keywordValue","multiple":false,"typeClass":"primitive","value":"single-cell TCR sequencing"}},{"keywordValue":{"typeName":"keywordValue","multiple":false,"typeClass":"primitive","value":"plaque"}}]},{"typeName":"publication","multiple":true,"typeClass":"compound","value":[{"publicationCitation":{"typeName":"publicationCitation","multiple":false,"typeClass":"primitive","value":"Circ Res\nDepuydt MAC, Schaftenaar FH, Prange KHM, Boltjes A, Hemme E, Delfos L, de Mol J, de Jong MJM, Bernabé Kleijn MNA, Peeters JAHM, Goncalves L, Wezel A, Smeets HJ, de Borst GJ, Foks AC, Pasterkamp G, de Winther MPJ, Kuiper J, Bot I, Slütter B. Single-cell T-cell Receptor sequencing of paired human atherosclerotic plaques and blood reveals autoimmune-like features of expanded effector T-cells. Nature Cardiovascular Research. 2022 t.b.d. doi: t.b.d.. t.b.d. PMID: t.b.d.."}}]},{"typeName":"depositor","multiple":false,"typeClass":"primitive","value":"van der Laan, Sander"},{"typeName":"dateOfDeposit","multiple":false,"typeClass":"primitive","value":"2022-12-09"}]},"dansDataVaultMetadata":{"displayName":"Data Vault Metadata","name":"dansDataVaultMetadata","fields":[{"typeName":"dansDataversePid","multiple":false,"typeClass":"primitive","value":"doi:10.34894/DDYKLL"},{"typeName":"dansDataversePidVersion","multiple":false,"typeClass":"primitive","value":"1.0"},{"typeName":"dansBagId","multiple":false,"typeClass":"primitive","value":"urn:uuid:64df4532-bb66-41c6-bc7e-f85b83192571"},{"typeName":"dansNbn","multiple":false,"typeClass":"primitive","value":"urn:nbn:nl:ui:13-363e814d-f204-4bc4-ae0c-15a7b2b0f7ce"}]}},"files":[{"description":"Approval Medical Ethics 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