Genomic DNA from normotrophic scar fibroblasts from patient 2 data from: Methylation profiling by genome tiling array

Experiment type: Methylation profiling by genome tiling array

Summary: 3mm punch biopsies were taken from a healed normotrophic scar and a contralateral matched control site in burn patients with a scar at least 1 year old. Fibroblasts were cultured from explants to passage 2 and DNA was extracted and run on methylation arrays to examine differences in scar and control fibroblast gene expression
Normotrophic scar maintains its abnormal scar phenotype for the rest of the patients life, long after the injury has healed. Differences in gene expression may reaveal target genes that can be modulated to improve scar appearance.

Overall design: 6 patients had normotrophic scar and matched control fibroblasts extracted and compared.

Sample type genomic

Source name Patient 2 Scar
Organism Homo sapiens
Characteristics Sex: Male
age (years): 29
time since injury (years): 3
Treatment protocol There were no treatments applied to the scar and control cells in vitro. DNA was bisulfite treated prior to processing on the chip
Growth protocol 3mm punch biopsies were taken from the forearm scar site and a matched site on the uninjured forearm by the attendant physician. Tissue was transported to the lab where it was placed in a petri dish and sliced into three equal sized potions. Pieces of the biopsy were then placed dermis side down in a T-25 (25 cm2) (Greiner Bio-One, Germany) culture flask without any media, and a drop of 100% foetal bovine serum (FBS) added to the surface of each piece. They were then cultured in DMEM with 10% FBS and 5% pen/strep until passage 2, at which point DNA and RNA was extracted.
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted using either the Promega Wizard SV Genomic DNA system (Patients 1 and 2, Promega, USA) or the QIAamp DNA mini kit system (Patients 3-6, Qiagen, Netherlands) as per manufacturer’s instructions
Label Cy3 and Cy5
Label protocol Standard Illumina protocol

Hybridization protocol bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol
Scan protocol Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
Description Normotrophic Scar Fibroblast DNA
Data processing Methylation data was imported from the raw files using Illumina® GenomeStudio and analysed using R statistics software, using the RnBeads package

实验类型：通过基因组平铺芯片（genome tiling array）开展甲基化谱分析

摘要：从瘢痕形成至少1年的烧伤患者的愈合后正常瘢痕（normotrophic scar）及对侧匹配对照部位采集3mm环钻活检组织，将外植体培养的成纤维细胞传至第2代，提取DNA并进行甲基化芯片检测，以分析瘢痕与对照成纤维细胞的基因表达差异。正常瘢痕会在患者余生中持续保持其异常瘢痕表型，远在损伤愈合之后。基因表达的差异或可揭示可被调控以改善瘢痕外观的靶基因。

实验设计：共纳入6名患者，分别采集其正常瘢痕及匹配对照的成纤维细胞并进行对比分析。

样本类型：基因组（genomic）样本

样本来源名称：患者2瘢痕组织

物种：智人（Homo sapiens）

样本特征：性别：男性；年龄（岁）：29；损伤后时间（年）：3

处理方案：体外实验中未对瘢痕及对照细胞施加任何处理。DNA在芯片上机前进行亚硫酸氢盐（bisulfite）处理。

培养方案：主治医师从前臂瘢痕部位及未损伤前臂的匹配部位采集3mm环钻活检组织。将组织转运至实验室后置于培养皿中，切割为三等份。将活检组织块真皮面朝下放置于T-25（25 cm²）（德国Greiner Bio-One公司）培养瓶中，不添加培养基，并在每块组织表面滴加100%胎牛血清（FBS）。随后将其置于含10% FBS及5%青链霉素的DMEM培养基中培养至第2代，此时提取DNA与RNA。

提取分子：基因组DNA（genomic DNA）

提取方案：基因组DNA提取分别采用Promega Wizard SV基因组DNA提取系统（患者1、2，美国Promega公司）或QIAamp DNA迷你试剂盒（患者3-6，荷兰Qiagen公司），严格按照制造商说明书操作。

标记：Cy3与Cy5

标记方案：采用标准Illumina标记流程。

杂交方案：将亚硫酸氢盐转化后的DNA进行扩增、片段化，采用标准Illumina流程杂交至Illumina Infinium人类甲基化27微珠芯片（Human Methylation27 Beadchip）。

扫描方案：采用BeadArray阅读器，按照Illumina官方推荐的扫描仪设置对芯片进行成像。

样本描述：正常瘢痕成纤维细胞DNA

数据处理：甲基化数据通过Illumina® GenomeStudio从原始文件导入，并使用R统计软件及RnBeads包进行分析。