Epigenomic analysis of formalin-fixed paraffin-embedded samples

Abstract

Disclosed herein are improved in situ methods for mapping the location of a protein on chromatin and DNA-based in situ methods for measuring transcription in a cell from a formalin-fixed paraffin-embedded (FFPE) sample. The methods can include steps of treating the FFPE sample to remove paraffin; permeabilizing the sample; contacting the sample with a first affinity reagent that specifically binds to a targeted chromatin protein or a protein involved in transcription regulation, wherein the first affinity reagent is coupled to a transposome comprising at least one transposase and a transposon; activating the at least one transposase under low ionic conditions, thereby cleaving and tagging chromatin DNA; excising the tagged DNA segment associated with the targeted chromatin protein or protein involved in transcription regulation; and determining the nucleotide sequence of the excised tagged DNA segment, thereby mapping the genomic location of the targeted protein on chromatin or transcriptional activity on chromatin.

Dependencies are inferred from the claim text.