Additional file 3 of Dimethyl fumarate reduces TNF and Plasmodium falciparum induced brain endothelium activation in vitro

Additional file 3. Differentially expressed transcripts in DMF pretreated TNF treated HBMVEC compared to TNF treatment. HBMVEC were preincubated with DMF (50 μM) for 1 h prior to the addition of TNF incubation (10 ng/ml) or TNF incubation alone for 6 h. Total RNA was extracted, reverse-transcribed, amplified and hybridized to a microarray. Gene expression profiles were generated using a robust multi-array average algorithm followed by quantile normalization and batch correction. Data represents three independent experiments, each done in triplicate. 348 transcripts were significantly differentially abundant between experimental groups using a Student’s t test and FDR (fold change > 2, FDR ≤ 0.01, p < 0.005).补充文件3：经富马酸二甲酯（Dimethyl Fumarate, DMF）预处理后再经肿瘤坏死因子（Tumor Necrosis Factor, TNF）处理的人脑微血管内皮细胞（Human Brain Microvascular Endothelial Cells, HBMVEC）与仅经TNF处理的HBMVEC之间的差异表达转录本。实验中，将HBMVEC先用50 μM的DMF预孵育1小时，随后加入10 ng/ml的TNF继续孵育6小时；对照组仅加入TNF孵育6小时。提取总RNA后，经逆转录、扩增步骤与微阵列芯片进行杂交。采用稳健多阵列平均算法生成基因表达谱，随后依次进行分位数归一化与批次校正。本数据集包含3次独立实验，每次实验均设置3个平行重复。通过学生t检验结合错误发现率（False Discovery Rate, FDR）进行显著性筛选，最终得到348个在两组间丰度存在显著差异的转录本（筛选标准为：倍数变化>2，错误发现率≤0.01，p值<0.005）。