Evaluation of the applicability of PAT-ChIP to eosin- or hematoxylin-stained tissue slides. Chromatin was extracted from four 10-μm tissue slides stained either with eosin or hematoxylin, or not stained (Ctrl), prepared starting from the same FFPE lung sample taken from a 9-month-old K-rasv12 transgenic mouse. Chromatin was then immunoprecipitated with the anti-H3K4me3 antibody and the resulting purified DNA analyzed by qPCR for enrichment at specific loci. (A) Evaluation of chromatin fragmentation by electrophoretic separation on 1.3% AGE and by ethidium bromide staining of purified input DNA. MKs, molecular weight markers. (B) Total amount of DNA obtained by PAT-ChIP by using an anti-H3K4me3 antibody, expressed as the ratio between bound and input DNA (percentage; mean values obtained from experiment conducted in triplicate). Mock, no antibody; *, not detectable. (C) Amplification of transcriptionally active (Actb and Gapdh) and inactive (Hapln1 and Col2a1) promoter regions by real-time qPCR (each sample amplified in triplicate). Enrichments of the promoter sequences associated with the indicated genes for H3K4me3 (Mock, no antibody) are expressed as the bound/input ratio (percentage).