Drop-ChIP/scChIP-seq
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.
Advantages:
- Analyzes chromatin states from single cells in a highly parallel manner
- Unique molecular barcoding reduces the risk posed by unspecific antibodies
Disadvantages:
- Data from each cell are sparse
Reagents:
Illumina Library prep and Array Kit Selector
Reviews:
Clark S. J., Lee H. J., Smallwood S. A., Kelsey G. and Reik W. Single-cell epigenomics: powerful new methods for understanding gene regulation and cell identity. Genome Biol. 2016;17:72
Wen L. and Tang F. Single-cell sequencing in stem cell biology. Genome Biol. 2016;17:71
Shin J., Ming G. L. and Song H. Decoding neural transcriptomes and epigenomes via high-throughput sequencing. Nat Neurosci. 2014;17:1463-1475
References:
Rotem A., Ram O., Shoresh N., et al. Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state. Nat Biotechnol. 2015;
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History: Drop-ChIP/scChIP-seq
Revision by sbrumpton on 2017-06-21 07:50:20 - Show/Hide
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.
Advantages:- Analyzes chromatin states from single cells in a highly parallel manner
- Unique molecular barcoding reduces the risk posed by unspecific antibodies
Disadvantages:- Data from each cell are sparse
Reagents:Illumina Library prep and Array Kit SelectorReviews:Clark S. J., Lee H. J., Smallwood S. A., Kelsey G. and Reik W. Single-cell epigenomics: powerful new methods for understanding gene regulation and cell identity. Genome Biol. 2016;17:72Wen L. and Tang F. Single-cell sequencing in stem cell biology. Genome Biol. 2016;17:71Shin J., Ming G. L. and Song H. Decoding neural transcriptomes and epigenomes via high-throughput sequencing. Nat Neurosci. 2014;17:1463-1475References:Rotem A., Ram O., Shoresh N., et al. Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state. Nat Biotechnol. 2015;