HEK and HeLa cells: transfection of siRNA directed against GFP versus mock transfection

We tested the most widely used control siRNA directed against GFP for off-target effects and found by genome-wide expression profiling that it deregulates in addition to GFP a set of endogenous target genes. The detected modulated mRNA had target sequences homologous to the siRNA as small as 9 bp in size. However, we found no restriction of sequence homology to 3'UTR of target genes. Keywords: RNAi knock down Two-condition experiment, siGFP transfected versus mock transfection, one replicate per array, one colour-switch per array

我们针对靶向绿色荧光蛋白（GFP）的最常用对照小干扰RNA（siRNA）开展了脱靶效应评估。通过全基因组表达谱分析，我们发现该对照siRNA除靶向GFP外，还会导致一组内源靶基因的表达失调。所检测到的受调控mRNA，其靶序列与该siRNA的同源序列长度可短至9个碱基对（bp）。但我们并未发现序列同源性仅局限于靶基因3'非翻译区（3'UTR）的现象。关键词：RNA干扰敲低（RNAi knock down）。两条件实验：转染siGFP组与模拟转染组，每块芯片设置一个重复样本，每块芯片进行一次荧光色彩切换。