Non-unique sequences and limited digestion of RNA cause false positives in ChIP-Chip experiments. A σ32 ChIP signal after long (two experiments, green and violet) and short RNase incubation (dark red). B σ32 ChIP signal for the yghJ region (Colors are as in A). C σ32 ChIP-Chip of E. coli grown at 30°C analyzed excluding non-unique sequences (blue) and including non-unique sequences (red). Inner three circles mark the position of peaks detected (similar coloring as for ChIP signals) and positions of non-unique sequences (green).