From: Laboratory methods to decipher epigenetic signatures: a comparative review
Technique | Scale | Cells | Advantages | Limitations | References |
---|---|---|---|---|---|
nChIP (1988) | High throughput | 106 ~ 107 | Recommended for high-affinity DNA binding proteins Proteins remain intact Good chromatin and protein recovery efficiency Bead-based immunoprecipitation | Time consuming (several days) Labor intensive (several precipitation steps) High variability in results Not recommended for non-histone proteins | |
XchIP (1984) | High throughput | 106 ~ 107 | Recommended for any weakly chromatin-associated proteins such as TFs Recommended where native protein is hard to prepare | Time consuming (several days) | [90] |
CChIP | Low throughput | 100 | Requires as few as 100 cells It takes two to three days | It takes two to three days Highly specific primers are required | [91] |
Q2 CHIP | Low throughput | 100,000 | Reduced steps Enhanced signal to noise ratio | Time consuming (several days) | [92] |
MicroChIP/μChIP (2007) | Low throughput | 10,000 | Applicable for genome-wide studies | Time consuming (several days) | [93] |
Fast CHIP (2006) | High throughput | 106 ~ 107 | The incubation time is decreased Several steps are reduced in protocol Preparation of PCR-ready template is reduced to 1 h | Suitable if only for large cell samples are available | [94] |
Matrix ChIP (2008) | High throughput | Â | Enhanced antibody binding capacity Requires minimal sampling Very Fast (1Â day) Can detect both Low and High-affinity proteins Automation is possible Includes high sensitivity High reproducibility | Â | [95] |