Profiling chromatin state by single-cell itChIP-seq [itChIP-seq]

We present a low-cost, generalizable ChIP-seq (itChIP), compatible to both low-input and single cells for profiling chromatin states. This method combines chromatin opening, simultaneous cellular indexing and chromatin tagmentation in a single tube. Single-cell itChIP data yield ~ 5000 unique reads per cell, sufficiently defining cell identifies and subpopulations of a given cell type. Our results demonstrate that itChIP is a generalizable technology for single-cell chromatin profiling of samples limited to ultra-low number of cells. Overall design: Based on Tn5 transposition of chromatin, the generalizable itChIP combines chromatin opening, simultaneous cellular indexing and chromatin tagmentation in a single tube.