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.

本数据集收录了配套发表论文中各项结果的原始支撑数据。下文将对本数据集所涵盖的实验内容进行简要说明。

研究背景：在子宫内刺激皮肤再生，将极大改善脊柱裂（spina bifida）的治疗效果。该病症因组织缺失导致脊髓外露，会对神经系统发育造成严重不良影响。临床通常通过手术闭合缺损部位，但该手段常会引发瘢痕形成与组织挛缩。既往研究表明，以肝素（heparin, HEP）、成纤维细胞生长因子2（fibroblast growth factor 2, FGF2）与血管内皮生长因子（vascular endothelial growth factor, VEGF）功能化修饰的I型多孔胶原（type I collagen, COL）支架（COL-HEP/GF），可在胎羊全层伤口模型中有效改善产前及产后的皮肤再生效果。

研究目标：明确植入COL（或COL-HEP/GF）支架两周后，愈合中的胎羊皮肤伤口的基因表达谱。本研究采用Affymetrix基因芯片（Affymetrix Microarrays）检测基因表达水平，并分别在表皮与真皮层中，鉴定未处理伤口、COL支架处理伤口以及COL-HEP/GF支架处理伤口之间的差异表达基因（differentially expressed genes, DEG）。通过上述差异表达基因，进一步揭示了该优化皮肤再生手段背后的核心生物学过程。

数据集内容：
1. 基因芯片原始数据：本研究通过Affymetrix GeneChips检测了植入COL（或COL-HEP/GF）生物材料两周后全层伤口的基因表达谱，并分别对表皮层与真皮层进行独立分析。本数据集收录了各芯片的基因表达强度原始文件（格式为Affymetrix标准.CEL格式），供后续使用者开展完整的数据分析。数据文件夹中还包含从芯片数据中提取的差异基因表达量Excel文件，按皮肤分层与处理组间比较进行分类整理。
2. 基因本体生物学过程注释结果：本研究通过免费在线数据库DAVID对差异表达基因列表进行富集分析，提取得到显著富集的生物学过程。本数据集收录的.txt文件包含了各皮肤分层与各组比较中，显著过度表达的生物学过程（以基因本体（gene ontology, GO）术语标注）。
3. 定量聚合酶链反应（qPCR）验证数据：本研究通过定量聚合酶链反应（quantitative polymerase chain reaction, qPCR）对基因芯片分析结果进行验证。从各组比较中选取上调幅度最高的差异表达基因，通过qPCR检测其表达水平。本数据集收录了各基因的原始qPCR检测数据。