{"status":"OK","data":{"id":510317,"identifier":"HWOSWP","persistentUrl":"https://doi.org/10.34894/HWOSWP","protocol":"doi","authority":"10.34894","separator":"/","publisher":"DataverseNL","publicationDate":"2025-09-10","storageIdentifier":"surf://10.34894/HWOSWP","effectiveDatasetFileCountLimit":10000,"datasetFileUploadsAvailable":9994,"datasetType":"dataset","locks":[],"latestVersion":{"id":31373,"datasetId":510317,"datasetPersistentId":"doi:10.34894/HWOSWP","datasetType":"dataset","storageIdentifier":"surf://10.34894/HWOSWP","versionNumber":1,"internalVersionNumber":47,"versionMinorNumber":0,"versionState":"RELEASED","latestVersionPublishingState":"RELEASED","deaccessionLink":"","lastUpdateTime":"2025-09-10T10:54:14Z","releaseTime":"2025-09-10T10:54:14Z","createTime":"2025-08-20T08:13:58Z","publicationDate":"2025-09-10","citationDate":"2025-09-10","effectiveDatasetFileCountLimit":10000,"datasetFileUploadsAvailable":9994,"license":{"name":"CC-BY-4.0","uri":"http://creativecommons.org/licenses/by/4.0","iconUri":"https://i.creativecommons.org/l/by/4.0/88x31.png"},"fileAccessRequest":true,"metadataBlocks":{"citation":{"displayName":"Citation Metadata","name":"citation","fields":[{"typeName":"title","multiple":false,"typeClass":"primitive","value":"SOX2 is a Potential Diagnostic Biomarker and Anticancer Target in Cutaneous Squamous Cell Carcinoma in Dystrophic Epidermolysis Bullosa: A Case Series Study"},{"typeName":"author","multiple":true,"typeClass":"compound","value":[{"authorName":{"typeName":"authorName","multiple":false,"typeClass":"primitive","value":"Harrs, Clara"},"authorAffiliation":{"typeName":"authorAffiliation","multiple":false,"typeClass":"primitive","value":"rug.nl"},"authorIdentifierScheme":{"typeName":"authorIdentifierScheme","multiple":false,"typeClass":"controlledVocabulary","value":"ORCID"},"authorIdentifier":{"typeName":"authorIdentifier","multiple":false,"typeClass":"primitive","value":"0000-0002-0034-911X"}},{"authorName":{"typeName":"authorName","multiple":false,"typeClass":"primitive","value":"Bolling, Maria Caroline"},"authorAffiliation":{"typeName":"authorAffiliation","multiple":false,"typeClass":"primitive","value":"rug.nl"},"authorIdentifierScheme":{"typeName":"authorIdentifierScheme","multiple":false,"typeClass":"controlledVocabulary","value":"ORCID"},"authorIdentifier":{"typeName":"authorIdentifier","multiple":false,"typeClass":"primitive","value":"0000-0003-2086-9363"}},{"authorName":{"typeName":"authorName","multiple":false,"typeClass":"primitive","value":"van den Akker, Peter C."},"authorAffiliation":{"typeName":"authorAffiliation","multiple":false,"typeClass":"primitive","value":"rug"},"authorIdentifierScheme":{"typeName":"authorIdentifierScheme","multiple":false,"typeClass":"controlledVocabulary","value":"ORCID"},"authorIdentifier":{"typeName":"authorIdentifier","multiple":false,"typeClass":"primitive","value":"0000-0002-3734-753X"}},{"authorName":{"typeName":"authorName","multiple":false,"typeClass":"primitive","value":"Koopman, Bart"},"authorAffiliation":{"typeName":"authorAffiliation","multiple":false,"typeClass":"primitive","value":"rug.nl"},"authorIdentifierScheme":{"typeName":"authorIdentifierScheme","multiple":false,"typeClass":"controlledVocabulary","value":"ORCID"},"authorIdentifier":{"typeName":"authorIdentifier","multiple":false,"typeClass":"primitive","value":"0000-0003-0873-9638"}},{"authorName":{"typeName":"authorName","multiple":false,"typeClass":"primitive","value":"Horváth, Barbara"},"authorAffiliation":{"typeName":"authorAffiliation","multiple":false,"typeClass":"primitive","value":"rug.nl"},"authorIdentifierScheme":{"typeName":"authorIdentifierScheme","multiple":false,"typeClass":"controlledVocabulary","value":"ORCID"},"authorIdentifier":{"typeName":"authorIdentifier","multiple":false,"typeClass":"primitive","value":"0000-0001-8559-3674"}},{"authorName":{"typeName":"authorName","multiple":false,"typeClass":"primitive","value":"Diercks, Gilles F.H."},"authorAffiliation":{"typeName":"authorAffiliation","multiple":false,"typeClass":"primitive","value":"rug.nl"},"authorIdentifierScheme":{"typeName":"authorIdentifierScheme","multiple":false,"typeClass":"controlledVocabulary","value":"ORCID"},"authorIdentifier":{"typeName":"authorIdentifier","multiple":false,"typeClass":"primitive","value":"0000-0001-8053-216X"}},{"authorName":{"typeName":"authorName","multiple":false,"typeClass":"primitive","value":"van Kempen, Leon C."},"authorAffiliation":{"typeName":"authorAffiliation","multiple":false,"typeClass":"primitive","value":"rug.nl"},"authorIdentifierScheme":{"typeName":"authorIdentifierScheme","multiple":false,"typeClass":"controlledVocabulary","value":"ORCID"},"authorIdentifier":{"typeName":"authorIdentifier","multiple":false,"typeClass":"primitive","value":"0000-0003-0646-0705"}}]},{"typeName":"datasetContact","multiple":true,"typeClass":"compound","value":[{"datasetContactName":{"typeName":"datasetContactName","multiple":false,"typeClass":"primitive","value":"Groningen Digital Competence Centre"},"datasetContactAffiliation":{"typeName":"datasetContactAffiliation","multiple":false,"typeClass":"primitive","value":"rug.nl"}}]},{"typeName":"dsDescription","multiple":true,"typeClass":"compound","value":[{"dsDescriptionValue":{"typeName":"dsDescriptionValue","multiple":false,"typeClass":"primitive","value":"The dataset consists of the data used for the publication ''SOX2 is a Potential Diagnostic Biomarker and Anticancer Target in Cutaneous Squamous Cell Carcinoma in Dystrophic Epidermolysis Bullosa: A Case Series Study''. For this article mRNA expression analysis and immunohistochemistry on formalin-fixed paraffin-embedded (FFPE) tissue samples of the following groups have been conducted:\n(1): cutaneous squamous cell carcinoma (cSCC) of patients with epidermolysis bullosa  (EB-cSCC; n=9)\n(2): UV-induced cSCC of patients without EB (UV-induced cSCC; n=10) \n(3): Pseudoepitheliomatous hyperplasia in EB-patients (EB-PEHs; n=7)\n\nSpecifically, the dataset consists of the results of the differential gene expression analysis of EB-cSCC vs. UV-induced cSCC (baseline) [Folder 1] and the Pathology slide specimen images (.ndpi files) of the SOX2 immunohistochemical expression of the aforementioned three groups [Folder 2.1; 2.2; 2.3]."},"dsDescriptionDate":{"typeName":"dsDescriptionDate","multiple":false,"typeClass":"primitive","value":"2025-08-25"}}]},{"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":"Differential expression analysis"}},{"keywordValue":{"typeName":"keywordValue","multiple":false,"typeClass":"primitive","value":"Immunohistochemical expression"}}]},{"typeName":"notesText","multiple":false,"typeClass":"primitive","value":"INFORMATION FROM README FILES FOR FOLDER 1 AND 2.1, 2.2, 2.3: \n\nAdditional metadata for folder 1 [mRNA expression data]: \nThis folder consists of the results of the differential expression data of the EB-cSCC vs. UV-induced cSCC (baseline). \nIn folder 1.1 all included genes are depicted of the Nanostring nCounter® PanCancer IO 360™ Panel (n=658) and in folder 1.2 only the 20 genes with the lowest FDR-adjusted p-values [BY.p.value] are included. \n\nDescription variables in the .csv files:\nColumn: \n1. name of the differentially expressed genes \n\nRows: \nB. Log2 fold change \nC.. Standard error [std error (log2)\nD. Lower confidence limit (log2)\nE. Upper confidence limit (log2)\nF. Linear fold change\nG. Lower confidence limit (linear)\nH. Upper confidence limit (linear)\nI. P-value\nJ. FDR-adjusted p-value [BY.p.value]\nK. Method for applying negative binomial regression model: (log-linear negative binomial model [lm.nb]\nL: Gene sets used for classification of genes if applicable \nM: Individual probe.ID for each gene used for mRNA expression analysis\n\n\nAdditional metadata for folder 2.1.2.2 and 2.3 [.ndpi files with pathology slide specimen images]:\n\nWhat is an .ndpi file and how to open it? \nA .ndpi file is a pathology slide specimen image created by a Hamamatsu slide scanner, in the case of this research with Hamamatsu Nanozoomer 2.0HT (Hamamatsu Photonic K.K., Japan). It contains a picture of a slide specimen, saved in a proprietary, TIFF-like format. NDPI files can be viewed in Hamamatsu's slide-viewing software, or in other slide-viewing applications. \n\nFor this research the .ndpi files were opened with Aperio Technologies ImageScope, version 12.4.3 (Leica Biosystems, Germany) and the QuPath application, version 0. 5.1 (Bankhead et al., 2017).  \n\nLinks to the recent versions of Aperio Technologies ImageScope and QuPath:  \nAperio Technologies ImageScope: https://www.leicabiosystems.com/en-nl/digital-pathology/manage/aperio-imagescope/  \n\nQuPath: https://qupath.github.io/  \nQuPath, step-by-step guides: https://qupath.readthedocs.io/en/stable/  \n\nOther application which can be used to open .ndpi files and view the Pathology images are  NetScope Viewer (Windows), NDPITools (cross-platform), or OpenSlide (cross-platform)."},{"typeName":"distributor","multiple":true,"typeClass":"compound","value":[{"distributorName":{"typeName":"distributorName","multiple":false,"typeClass":"primitive","value":"DataverseNL network"},"distributorAffiliation":{"typeName":"distributorAffiliation","multiple":false,"typeClass":"primitive","value":"DANS"},"distributorAbbreviation":{"typeName":"distributorAbbreviation","multiple":false,"typeClass":"primitive","value":"DVNL"},"distributorURL":{"typeName":"distributorURL","multiple":false,"typeClass":"primitive","value":"https://dataverse.nl/"}}]},{"typeName":"depositor","multiple":false,"typeClass":"primitive","value":"Silva Correia Alves, Ana"},{"typeName":"dateOfDeposit","multiple":false,"typeClass":"primitive","value":"2025-08-20"},{"typeName":"kindOfData","multiple":true,"typeClass":"primitive","value":["Differential expression analysis [Folder 1]","Pathology slide specimen images for analysis of immunohistochemistry [Folder 2.1; 2.2; 2.3]"]},{"typeName":"software","multiple":true,"typeClass":"compound","value":[{"softwareName":{"typeName":"softwareName","multiple":false,"typeClass":"primitive","value":"R-based nSolver Analysis Software (NanoString Technologies)"},"softwareVersion":{"typeName":"softwareVersion","multiple":false,"typeClass":"primitive","value":"Version 4.0"}},{"softwareName":{"typeName":"softwareName","multiple":false,"typeClass":"primitive","value":"nSolver Advanced analysis plugin"},"softwareVersion":{"typeName":"softwareVersion","multiple":false,"typeClass":"primitive","value":"(version 2.0.1.34)"}}]}]},"dansDataVaultMetadata":{"displayName":"Data Vault Metadata","name":"dansDataVaultMetadata","fields":[{"typeName":"dansDataversePid","multiple":false,"typeClass":"primitive","value":"doi:10.34894/HWOSWP"},{"typeName":"dansDataversePidVersion","multiple":false,"typeClass":"primitive","value":"1.0"},{"typeName":"dansBagId","multiple":false,"typeClass":"primitive","value":"urn:uuid:56f5844e-a178-46dd-98c7-fd022d882184"},{"typeName":"dansNbn","multiple":false,"typeClass":"primitive","value":"urn:nbn:nl:ui:13-8114c097-fde9-4929-8bcf-9821f71026ac"}]}},"files":[{"description":"Results of the differential expression analysis of EB-cSCC vs. UV-induced cSCC (baseline) based on the mRNA expression profiling with Nanostring nCounter.","label":"Folder 1.mRNA.Nanostring.expression data.zip","restricted":false,"version":4,"datasetVersionId":31373,"dataFile":{"id":512986,"persistentId":"","filename":"Folder 1.mRNA.Nanostring.expression data.zip","contentType":"application/zip","friendlyType":"ZIP Archive","filesize":25647,"description":"Results of the differential expression analysis of EB-cSCC vs. UV-induced cSCC (baseline) based on the mRNA expression profiling with Nanostring nCounter.","storageIdentifier":"surf://store:198e2c4e053-2f0301d5d723","rootDataFileId":-1,"checksum":{"type":"SHA-1","value":"9d53eeed00f0a85b8f4c8c0ef13411305626b946"},"tabularData":false,"creationDate":"2025-08-25","publicationDate":"2025-09-10","lastUpdateTime":"2025-09-10T10:54:14Z","fileAccessRequest":true}},{"description":"Pathology slide specimen images (.ndpi files) of the SOX2 immunohistochemical expression of the cSCC in EB (EB-cSCC; n=9). 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