{"status":"OK","data":{"id":314561,"identifier":"4IKE3T","persistentUrl":"https://doi.org/10.34894/4IKE3T","protocol":"doi","authority":"10.34894","separator":"/","publisher":"DataverseNL","publicationDate":"2022-10-20","storageIdentifier":"surf://10.34894/4IKE3T","effectiveDatasetFileCountLimit":10000,"datasetFileUploadsAvailable":9996,"datasetType":"dataset","locks":[],"latestVersion":{"id":24376,"datasetId":314561,"datasetPersistentId":"doi:10.34894/4IKE3T","datasetType":"dataset","storageIdentifier":"surf://10.34894/4IKE3T","versionNumber":1,"internalVersionNumber":19,"versionMinorNumber":0,"versionState":"RELEASED","latestVersionPublishingState":"DRAFT","deaccessionLink":"","lastUpdateTime":"2022-10-20T05:58:02Z","releaseTime":"2022-10-20T05:58:02Z","createTime":"2022-10-18T10:34:32Z","publicationDate":"2022-10-20","citationDate":"2022-10-20","effectiveDatasetFileCountLimit":10000,"datasetFileUploadsAvailable":9996,"termsOfUse":"The standard Data Sharing Agreement (DSA) of the UMC Utrecht must be signed without adjustments. 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","fileAccessRequest":false,"metadataBlocks":{"citation":{"displayName":"Citation Metadata","name":"citation","fields":[{"typeName":"title","multiple":false,"typeClass":"primitive","value":"Athero-Express Biobank Study (database including clinical data)"},{"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":"Gerard Pasterkamp"},"authorAffiliation":{"typeName":"authorAffiliation","multiple":false,"typeClass":"primitive","value":"UMC Utrecht"},"authorIdentifierScheme":{"typeName":"authorIdentifierScheme","multiple":false,"typeClass":"controlledVocabulary","value":"ORCID"}},{"authorName":{"typeName":"authorName","multiple":false,"typeClass":"primitive","value":"Gert Jan de Borst"},"authorAffiliation":{"typeName":"authorAffiliation","multiple":false,"typeClass":"primitive","value":"UMC Utrecht"},"authorIdentifierScheme":{"typeName":"authorIdentifierScheme","multiple":false,"typeClass":"controlledVocabulary","value":"ORCID"}},{"authorName":{"typeName":"authorName","multiple":false,"typeClass":"primitive","value":"Dominique P.V. de Kleijn"},"authorAffiliation":{"typeName":"authorAffiliation","multiple":false,"typeClass":"primitive","value":"UMC Utrecht"},"authorIdentifierScheme":{"typeName":"authorIdentifierScheme","multiple":false,"typeClass":"controlledVocabulary","value":"ORCID"}}]},{"typeName":"datasetContact","multiple":true,"typeClass":"compound","value":[{"datasetContactName":{"typeName":"datasetContactName","multiple":false,"typeClass":"primitive","value":"dLAB Data Management"},"datasetContactAffiliation":{"typeName":"datasetContactAffiliation","multiple":false,"typeClass":"primitive","value":"UMC Utrecht"}},{"datasetContactName":{"typeName":"datasetContactName","multiple":false,"typeClass":"primitive","value":"Sander W. van der Laan"},"datasetContactAffiliation":{"typeName":"datasetContactAffiliation","multiple":false,"typeClass":"primitive","value":"UMC Utrecht"}}]},{"typeName":"dsDescription","multiple":true,"typeClass":"compound","value":[{"dsDescriptionValue":{"typeName":"dsDescriptionValue","multiple":false,"typeClass":"primitive","value":"<strong>Background</strong></br>\n<strong>The Athero-Express Biobank Study (AE)</strong> 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) at two Dutch tertiary referral centers. Details of the study design were described <a href=\"https://pubmed.ncbi.nlm.nih.gov/15678794/\" target=\"_blank\">before</a>. Briefly, blood and plaque material were obtained during endarterectomy and stored at -80℃; plaque material is routinely used for <a href=\"https://doi.org/10.1161/STROKEAHA.110.607382\" target=\"_blank\">standardised (immuno)histochemical analysis</a>. We quantitatively scored the number of macrophages (CD68) and smooth muscle cells (SMCs, α‐actin), as percentage of the microscope field area by computerised analysis. Intraplaque vessel density (CD34) was assessed as the average number per 3 hotspots. Intraplaque haemorrhage (IPH) was scored as no/yes using a hematoxylin and eosin staining (HE). Intraplaque fat was defined as less or more than 40% fat per total plaque area using HE. The amount of calcification (using HE) and collagen (picrosirius red) were binary scored as no/minor vs. moderate/heavy staining. Assessment of overall plaque vulnerability was performed as previously described by <a href=\"https://pubmed.ncbi.nlm.nih.gov/16376194/\" target=\"_blank\">Verhoeven <em>et al.</em></a> All histological observations were performed by the same dedicated technician and interobserver analyses <a href=\"https://pubmed.ncbi.nlm.nih.gov/17950565/\" target=\"_blank\">have been reported previously</a>. Clinical data is collected through standardised questionnaires and supplemented by querying electronic health records when needed.</br>\n</br>\nEthical approval for this study (TME/C-01.18) was provided by the Medical Research Ethics Committee of University Medical Center Utrecht, Utrecht, The Netherlands on 10 April 2002, and all research was conducted according to the principles of the Declaration of Helsinki (59th amendment, Seoul 2008) and in accordance with the Dutch Medical Research Involving Human Subjects Act (WMO). </br>\n</br>\n<b>Important notice on availability of data</b></br>\n- Whole-slide images (WSI) are available for the (immuno)histochemical stainings. The amount of data is huge, on average 1Gb size per WSI. These are accessible through <a href=\"https://doi.org/10.34894/QI135J\" target=\"_blank\"><strong>ExpressScan</strong></a>.</br>\n- Single-cell RNA sequencing data from <em>plaques</em> are accessible through <a href=\"https://doi.org/10.34894/TYHGEF\" target=\"_blank\">this repository</a>.</br>\n- Bulk (whole tissue) RNA sequencing data from <em>plaques</em> are accessible through <a href=\"https://doi.org/10.34894/D1MDKL\" target=\"_blank\">this repository</a>.</br>\n- Genetic (GWAS chip) data are described <a href=\"http://dx.doi.org/10.1161/CIRCGEN.118.002115\" target=\"_blank\">here</a> and  accessible through <a href=\"#\" target=\"_blank\">this repository [NOT AVAILABLE YET]</a>.</br>\n- ExomeChip data are described <a href=\"http://dx.doi.org/10.1073/pnas.1616301114\" target=\"_blank\">here</a> and accessible through <a href=\"#\" target=\"_blank\">this repository [NOT AVAILABLE YET]</a>.</br>\n- DNA methylation array data from <em>plaques</em> are described <a href=\"http://dx.doi.org/10.1161/CIRCGEN.117.002030\" target=\"_blank\">here</a> and  accessible through <a href=\"#\" target=\"_blank\">this repository [NOT AVAILABLE YET]</a>.</br>\n</br>\nThere are restrictions on use by commercial parties, and on sharing openly based on (inter)national laws and regulations and the written informed consent. Therefore these data (and additional clinical data) are only available upon discussion and signing a Data Sharing Agreement (see Terms of Access) and within a specially designed UMC Utrecht provided environment.</br></br>"},"dsDescriptionDate":{"typeName":"dsDescriptionDate","multiple":false,"typeClass":"primitive","value":"2022-10-18"}}]},{"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":"plaque"}},{"keywordValue":{"typeName":"keywordValue","multiple":false,"typeClass":"primitive","value":"endarterectomy"}}]},{"typeName":"publication","multiple":true,"typeClass":"compound","value":[{"publicationCitation":{"typeName":"publicationCitation","multiple":false,"typeClass":"primitive","value":"<a href=\"http://dx.doi.org/10.1161/STROKEAHA.110.607382\" target=\"_blank\">van Lammeren, G. W. <em>et al.</em></a> Atherosclerotic Plaque Vulnerability as an Explanation for the Increased Risk of Stroke in Elderly Undergoing Carotid Artery Stenting. <strong>Stroke</strong> 42, 2550–2555 (2011).</br>"},"publicationIDType":{"typeName":"publicationIDType","multiple":false,"typeClass":"controlledVocabulary","value":"doi"},"publicationIDNumber":{"typeName":"publicationIDNumber","multiple":false,"typeClass":"primitive","value":"10.1161/STROKEAHA.110.607382"},"publicationURL":{"typeName":"publicationURL","multiple":false,"typeClass":"primitive","value":"http://dx.doi.org/10.1161/STROKEAHA.110.607382"}},{"publicationCitation":{"typeName":"publicationCitation","multiple":false,"typeClass":"primitive","value":"<a href=\"http://dx.doi.org/10.1007/s10564-004-2304-6\" target=\"_blank\">Verhoeven, B. A. N. <em>et al.</em></a> Athero-express: differential atherosclerotic plaque expression of mRNA and protein in relation to cardiovascular events and patient characteristics. Rationale and design. <strong>Eur. J. Epidemiol.</strong> 19, 1127–1133 (2004).</br>"},"publicationIDType":{"typeName":"publicationIDType","multiple":false,"typeClass":"controlledVocabulary","value":"doi"},"publicationIDNumber":{"typeName":"publicationIDNumber","multiple":false,"typeClass":"primitive","value":"10.1007/s10564-004-2304-6"},"publicationURL":{"typeName":"publicationURL","multiple":false,"typeClass":"primitive","value":"http://dx.doi.org/10.1007/s10564-004-2304-6"}},{"publicationCitation":{"typeName":"publicationCitation","multiple":false,"typeClass":"primitive","value":"<a href=\"http://dx.doi.org/10.1016/j.jvs.2005.08.009\" target=\"_blank\">Verhoeven, B. A. N. <em>et al.</em></a> Carotid atherosclerotic plaques in patients with transient ischemic attacks and stroke have unstable characteristics compared with plaques in asymptomatic and amaurosis fugax patients. <strong>J. Vasc. Surg.</strong> 42, 1075–1081 (2005). </br>"},"publicationIDType":{"typeName":"publicationIDType","multiple":false,"typeClass":"controlledVocabulary","value":"doi"},"publicationIDNumber":{"typeName":"publicationIDNumber","multiple":false,"typeClass":"primitive","value":"10.1016/j.jvs.2005.08.009"},"publicationURL":{"typeName":"publicationURL","multiple":false,"typeClass":"primitive","value":"http://dx.doi.org/10.1016/j.jvs.2005.08.009"}},{"publicationCitation":{"typeName":"publicationCitation","multiple":false,"typeClass":"primitive","value":"<a href=\"http://dx.doi.org/10.1016/j.jvs.2007.08.018\" target=\"_blank\">Hellings, W. E. <em>et al.</em></a> Intraobserver and interobserver variability and spatial differences in histologic examination of carotid endarterectomy specimens. <strong>J. Vasc. Surg.</strong> 46, 1147–1154 (2007).</br>"},"publicationIDType":{"typeName":"publicationIDType","multiple":false,"typeClass":"controlledVocabulary","value":"doi"},"publicationIDNumber":{"typeName":"publicationIDNumber","multiple":false,"typeClass":"primitive","value":"10.1016/j.jvs.2007.08.018"},"publicationURL":{"typeName":"publicationURL","multiple":false,"typeClass":"primitive","value":"http://dx.doi.org/10.1016/j.jvs.2007.08.018"}},{"publicationCitation":{"typeName":"publicationCitation","multiple":false,"typeClass":"primitive","value":"<a href=\"http://dx.doi.org/10.1161/CIRCGEN.118.002115\" target=\"_blank\">van der Laan, S. W. <em>et al.</em></a> Genetic Susceptibility Loci for Cardiovascular Disease and Their Impact on Atherosclerotic Plaques. <strong>Circ Genom Precis Med</strong> 11, e002115 (2018).</br>"},"publicationIDType":{"typeName":"publicationIDType","multiple":false,"typeClass":"controlledVocabulary","value":"doi"},"publicationIDNumber":{"typeName":"publicationIDNumber","multiple":false,"typeClass":"primitive","value":"10.1161/CIRCGEN.118.002115"},"publicationURL":{"typeName":"publicationURL","multiple":false,"typeClass":"primitive","value":"http://dx.doi.org/10.1161/CIRCGEN.118.002115"}},{"publicationCitation":{"typeName":"publicationCitation","multiple":false,"typeClass":"primitive","value":"<a href=\"http://dx.doi.org/10.1161/CIRCGEN.117.002030\" target=\"_blank\">Siemelink, M. A. <em>et al.</em></a> Smoking is Associated to DNA Methylation in Atherosclerotic Carotid Lesions. Circ Genom Precis Med 11, e002030 (2018)"},"publicationIDType":{"typeName":"publicationIDType","multiple":false,"typeClass":"controlledVocabulary","value":"doi"},"publicationIDNumber":{"typeName":"publicationIDNumber","multiple":false,"typeClass":"primitive","value":"10.1161/CIRCGEN.117.002030"},"publicationURL":{"typeName":"publicationURL","multiple":false,"typeClass":"primitive","value":"http://dx.doi.org/10.1161/CIRCGEN.117.002030"}},{"publicationCitation":{"typeName":"publicationCitation","multiple":false,"typeClass":"primitive","value":"<a href=\"http://dx.doi.org/10.1073/pnas.1616301114\" target=\"_blank\">Malik, R. <em>et al.</em></a> Common coding variant in SERPINA1 increases the risk for large artery stroke. <strong>Proc. Natl. Acad. Sci. U. S. 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