Droplet-Based Single-Cell Chromatin Immunoprecipitation Sequencing

Drop-ChIP or scChIP-seq analyzes the chromatin states of single cells by using microfluidics, unique molecular barcodes, and NGS (Rotem et al., 2015). In this method, single cells are isolated into droplets containing lysis buffer and micrococcal nuclease (MNase), and then fused to a droplet carrying distinct oligonucleotides. These oligonucleotides contain the sequences for cell-specific barcodes, sequencing adapters, and restriction sites. In addition, DNA ligase is fused with the droplet to complete the tagging process. Next, carrier chromatin is introduced into the pooled droplets before chromatin immunoprecipitation. Library preparation is carried out according to standard ChIP-Seq procedures before sequencing.


  • Analyzes chromatin states from single cells in a highly parallel manner
  • Unique molecular barcoding reduces the risk posed by unspecific antibodies


  • Data from each cell are sparse


Illumina Library prep and Array Kit Selector


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Rotem A., Ram O., Shoresh N., et al. Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state. Nat Biotechnol. 2015;