Table 1. Scheme of ChIP-chip hybridization per sample.

Hybridization #	Hybridized Templates	Target genes
Hybridization 1	input-1 (Alexa 647)/IgG-1(Alexa 555)	unspecific genes
Hybridization 2	input-2 (Alexa 647)/IgG-2(Alexa 555)
Hybridization 3	input-1 (Alexa 647)/ERG-1(Alexa 555)	ERG enriched genes
Hybridization 4	input-2 (Alexa 647)/ERG-2(Alexa 555)

For each primary sample four hybridizations were carried out. IgG-enriched DNA was paired with input-DNA and ERG-enriched with input-DNA. DNA-mixtures were hybridized to a promoter chip array. Thus, genes identified as enriched in the IgG/input hybridizations (hybridization 1 and 2) were treated as unspecifically enriched genes and those identified in the ERG/input hybridizations (hybridization 3 and 4) were regarded as ERG-enriched genes. Finally, only those genes that were enriched in hybridization 3 and 4 only were regarded as putative ERG target genes.