Collagen-heparin-FGF2-VEGF scaffolds induce a regenerative gene expression profile in a fetal sheep wound model: research data underlying the associated publication

This data collection contains data underlying the results published in the accompanying publication. Below is a short explanation of the experiment the content of the collection. Background: Stimulating skin regeneration in utero would greatly benefit treatment outcome of spina bifida, where missing tissues expose the spinal cord leading to detrimental effects on neurological development. Surgical closure of the defects often lead to scarring and contractures. Previous research demonstrated that porous type I collagen (COL) scaffold, functionalized with heparin (HEP), fibroblast growth factor 2 (FGF2) and vascular endothelial growth factor (VEGF) (COL-HEP/GF) improved pre- and postnatal skin regeneration in a fetal sheep full thickness wound model. Goal of the research: determining the gene expression profiles of healing fetal skin wounds two weeks after implantation of the COL(-HEP/GF) scaffolds. Gene expression was measured using Affymetrix Microarrays and differentially expressed genes (DEG) were identified in the epidermis and dermis between untreated wounds, COL-treated wounds and wounds treated with COL-HEP/GF. From these DEG’s, the biological processes underlying the improved skin regeneration were uncovered. Content of the collection: - Microarray data. The gene expression profiles of full thickness wounds 2 weeks after implantation of the COL(-HEP/GF) biomaterial was investigated using Affymetrix GeneChips. The epidermis and dermis skin layer was analysed separately. The original files (in Affymetrix standard .CEL format) are the gene expression intensity readouts of each individual chip, and these are present in this collection in case re-users want to perform a full analysis of the data. The data folder contains Excel files with the differential gene expression values extracted from the chips, organized between the two skin layers and comparisons between treatments. - Biological gene ontology processes. These processes were identified using the freely accessible online database DAVID, where enriched biological processes were extracted from the lists of DEGs. The .text files contain all biological processes (labeled with gene ontology (GO) terms) found to be overrepresented in each skin layer and comparison. - qPCR validation. The results of the microarray analysis were validated via quantitative polymerase chain reaction (qPCR). Top-upregulated DEGs were selected from each comparison and their expression levels were investigated through qPCR. The raw qPCR data for each gene is included in the collection.