Table 2.
Methylome sequencing methods with brief explanations and differences in workflows.
| Method | Protocol Base | Sorting | Average CpG Coverage | Comments | Refs |
|---|---|---|---|---|---|
| scRRBS | RRBS | Mechanical separation | 1.02 × 106 (40% of total 2.5 × 106) | Integrated all steps in single-tube reaction without including any purification steps prior to the bisulfite treatment step | 22 |
| scBS | Bisulfite treatment | Flow cytometry | 3.7 × 106 | First method to use postbisulfite adapter tagging | 26 |
| scWGBS | Bisulfite treatment | FACS | ~ 106 | Used postbisulfite adapter tagging | 28 |
| MID-RRBS | RRBS | FACS | 3.5 ~ 23.1 × 104 | Conducted RRBS method on a microfluidic device | 36 |
| sn-mC-seq | Bisulfite treatment | FANS | 22.2 ± 5.79% (Genome wide coverage) | Single nuclei-based method/used random priming | 30 |
| sn-mC-seq2 | Bisulfite treatment | FANS | ~30.8 ± 7.5% (Genome wide coverage) | Used RP-H (H = A, T, C) random primers for destabilizing primer hybridization, incorporated dephosphorylation step to inactivate dNTP | 31 |
| sci-MET | Bisulfite treatment | FANS | 0.05 ~ 7% (human) | Used combinatorial indexing | 33 |
| sci-METv2 | Bisulfite treatment | FANS | ~2.2 × 106(LA) ~0.3 × 106(SL) (human) | Two improved versions of sci-MET: sciMETv2.LA (linear amplification, accuracy), sciMETv2.SL (splint ligation, speed) | 34 |
| scSPLAT | Bisulfite treatment | FACS | At most 20 ~ 40% of human cell | Used RP-H for second strand synthesis and used splinted dsDNA adapters before PCR step | 32 |
| Msc-RRBS | RRBS | FACS (By cell cycle) | ~0.9 × 106 (Human) | Inline barcode single-well enzymatic reaction | 29 |
| sci-EM | Enzymatic conversion | FANS | Not specified | Combined combinatorial indexing with enzymatic conversion | 35 |