Evaluation of the applicability of PAT-ChIP to core needle biopsies (CNBs). Chromatin was extracted from one CNB or from a pool of four CNBs (0.6-mm diameter, 1-mm thickness) and from a pool of four FFPE tissue slides (sections, 10-μm thick) deriving from the same FFPE sample of mouse leukemic spleen. Chromatin was immunoprecipitated with an anti-H3K4me3 antibody, and the resulting purified DNA was analyzed by qPCR for enrichment at specific loci. (A) Evaluation of chromatin fragmentation by electrophoretic separation on 1.3% agarose gel electrophoresis (AGE) followed by ethidium bromide staining of purified input DNA. MKs, molecular weight markers. (B) Total amount of DNA obtained by PAT-ChIP 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).