Technology (single cell) | Information | Throughput (no. cells) | Strength | Limitation | Ref. | Year |
---|---|---|---|---|---|---|
RNA sequencing | Transcriptome | High (>1000) | Resolution | Low mRNA detection limit | 2009 | |
Amplification bias | ||||||
In situ RNA sequencing | Transcriptome with RNA localization | High (>1000) | Colocalization of locus and transcript | Time-consuming | 2014 | |
Abundance of rRNA transcripts | ||||||
Selective towards active gene | ||||||
ChIP sequencing | Protein association with the genome | High (>1000) | Reduced cost of ChIP assay | Antibody-dependent | [40] | 2015 |
Data sparsity/low coverage | ||||||
Hi-C | Global chromatin contact maps | Low (<100) | Global view of the genome | Data sparsity/low coverage | [35] | 2013 |
DamID | Lamina-associated domains | Medium (<200) | No need for antibody | Proximity assay | [36] | 2015 |
 |  |  |  | Relative low resolution |  |  |
ATAC sequencing | Genome accessibility | Medium (<500) | Resolution | Recovery of ATAC-seq DNA fragments | 2015 | |
Bisulfite sequencing (BiS) | DNA methylation | Medium (<400) | Base resolution | DNA amplification before bisulfite conversion | 2014 | |
Cost | ||||||
Reduced-representation BiS | DNA methylation | Low (<100) | Sensitivity | Low coverage | 2013 |