A TGFB Responsive Gene Expression Signature is Associated With More Severe Skin and Lung Disease in Diffuse Scleroderma. Homo sapiens

Primary dermal fibroblasts from patients with dSSc and healthy controls were treated with TGF beta for up to 24h and the genome-wide patterns of gene expression measured on DNA microarrays. 894 genes were identified as TGF beta-responsive in 4 independent cultures of dermal fibroblasts (2 healthy control and 2 dSSc patients). The 894 genes in the TGF beta-responsive signature are associated with induction of growth factor signaling, collagen synthesis and extracellular matrix deposition. Overall design: Common reference design; we used Universal Human Reference RNA (Stratagene) as our reference for every array; For every hybridization sample RNA was always labeled with Cy3, and reference RNA was always labeled with Cy5 All processed data is displayed as log2 of the LOWESS-normalized Cy5/Cy3 ratio and was multiplied by negative 1 for analysis in the associated publication.

本数据集的样本来源于弥漫性皮肤型系统性硬化症（diffuse cutaneous systemic sclerosis, dSSc）患者与健康对照的原代皮肤成纤维细胞，将上述细胞经转化生长因子β（transforming growth factor beta, TGF-β）处理至多24小时后，通过DNA微阵列（DNA microarray）检测全基因组基因表达谱。在4组独立培养的皮肤成纤维细胞（2组来自健康对照，2组来自dSSc患者）中，共有894个基因被鉴定为TGF-β应答基因。该TGF-β应答特征中的894个基因与生长因子信号通路激活、胶原蛋白合成及细胞外基质沉积过程密切相关。

实验设计概述：本研究采用通用参考设计方案，以通用人类参考RNA（Universal Human Reference RNA, Stratagene）作为所有芯片的对照参考样本；每一例杂交样本的RNA均采用Cy3荧光标记，参考RNA则统一以Cy5荧光标记。所有预处理后的数据以局部加权回归散点平滑（LOWESS）归一化后的Cy5/Cy3比值的log₂转换值呈现，且为适配相关发表论文的分析需求，已将该数值乘以-1。