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

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 Overall design: Two-condition experiment, siGFP transfected versus mock transfection, one replicate per array, one colour-switch per array