Drop-ChIP/scChIP-Seq

Drop-ChIP/scChIP-Seq

Droplet-based single-cell chromatin immune-precipitation sequencing (Drop-ChIP or scChIP-seq) analyzes the chromatin states of single-cells by utilizing microfluidics, unique molecular barcodes, and next-generation sequencing.

Single-cells are first isolated into droplets containing lysis buffer and MNase and then fused to a droplet carrying distinct oligonucleotides. These oligonucleotides contain the sequences for cell-specific barcodes, sequencing adaptors, and restriction sites. DNA ligase is also fused with the droplet to complete the tagging process. Then, carrier chromatins are introduced into the pooled droplets before chromatin immune-precipitation. Library preparation is carried out according to ChIP-Seq procedures before sequencing.

Pros:

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

Cons:

• The data from each cell is sparse

• Drop-ChIP/scChIP-Seq: Rotem A., Ram O., Shoresh N., Sperling R. A., Goren A., et al. (2015) Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state. Nat Biotechnol

1. Rotem A., Ram O., Shoresh N., Sperling R. A., Goren A., et al. (2015) Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state. Nat Biotechnol