Experimental validation of ChIP-Seq. A) Normalized IP ratio (arbitrary units) of corresponding DNA sequences belonging to significant peaks of 7 representative genes found in the present analysis. The NUE element of rat Nis (NIS) was used as a positive control while an unspecific sequence of the same Nis promoter (NIS-) was used as a negative control. B) Relative expression assessed by means of qRT-PCR of 7 (upper pannel) and 4 (lower pannel) genes differentially down- and upregulated in Pax8-silenced PCCl3 cells (siRNA Pax8) vs. wild type (wt)/siScramble (Scramble) cells, respectively. As a Pax8-dependent positive control, we evaluated Nis mRNA expression levels.