Profiling chromatin state by single-cell itChIP-seq [ATAC-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. ATAC-seq was processed with 50K mouse embryonic cells as previously described. Tn5-MEA/B was used to tagment the native chromatin.