DOI: 10.34894/hwoswp
title: SOX2 is a Potential Diagnostic Biomarker and Anticancer Target in Cutaneous Squamous Cell Carcinoma in Dystrophic Epidermolysis Bullosa: A Case Series Study

description: 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:
(1): cutaneous squamous cell carcinoma (cSCC) of patients with epidermolysis bullosa (EB-cSCC; n=9)
(2): UV-induced cSCC of patients without EB (UV-induced cSCC; n=10) 
(3): Pseudoepitheliomatous hyperplasia in EB-patients (EB-PEHs; n=7)

Specifically, 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].
description: INFORMATION FROM README FILES FOR FOLDER 1 AND 2.1, 2.2, 2.3: 

Additional metadata for folder 1 [mRNA expression data]: 
This folder consists of the results of the differential expression data of the EB-cSCC vs. UV-induced cSCC (baseline). 
In 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. 

Description variables in the .csv files:
Column: 
1. name of the differentially expressed genes 

Rows: 
B. Log2 fold change 
C.. Standard error [std error (log2)
D. Lower confidence limit (log2)
E. Upper confidence limit (log2)
F. Linear fold change
G. Lower confidence limit (linear)
H. Upper confidence limit (linear)
I. P-value
J. FDR-adjusted p-value [BY.p.value]
K. Method for applying negative binomial regression model: (log-linear negative binomial model [lm.nb]
L: Gene sets used for classification of genes if applicable 
M: Individual probe.ID for each gene used for mRNA expression analysis


Additional metadata for folder 2.1.2.2 and 2.3 [.ndpi files with pathology slide specimen images]:

What is an .ndpi file and how to open it? 
A .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. 

For 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). 

Links to the recent versions of Aperio Technologies ImageScope and QuPath: 
Aperio Technologies ImageScope: https://www.leicabiosystems.com/en-nl/digital-pathology/manage/aperio-imagescope/ 

QuPath: https://qupath.github.io/ 
QuPath, step-by-step guides: https://qupath.readthedocs.io/en/stable/ 

Other 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).
description: R-based nSolver Analysis Software (NanoString Technologies), Version 4.0
description: nSolver Advanced analysis plugin, (version 2.0.1.34)