PAT-ChIP-Seq: a novel tool for the epigenetic profiling of formaldehyde-fixed and paraffin-embedded (FFPE) pathology samples

Epigenetic alterations in the pattern of DNA and histone modifications play a crucial role in cancer development. Analysis of patient samples, however, is hampered by technical limitations in the study of chromatin structure from pathology archives that typically consist of heavily fixed, paraffin-embedded material. Overall design: ChIP assays (with anti-H3K4me3 and anti-H3K27me3 antibodies) were performed by using formaldehyde-fixed paraffin-embedded (FFPE) mouse spleen sections (half portion of the spleen) and comparing it to the canonical ChIP procedure applied by using isolated cells from the other portion of the same spleen.