Compilation of UHMW DNA extraction methods for UL sequencing, optimized in human GM12878 cells
| Without kits (phenol-based) | Without kits (phenol-free) | Kit-based | |||||
|---|---|---|---|---|---|---|---|
| Quick's phenol protocol Quick 2018 | Logsdon's phenol protocol Logsdon et al. 2021 | Phenol + glass beads | CTAB or SDS Lysis + glass beads | CTAB–CoHex Lysis + glass beads | NEB Monarch Cell & Blood Kit | Circulomics Nanobind CBB Big DNA Kit | |
| A | B | C | D | E | F | G | |
| Standard cell input | 50 million | 20–70 million | 1–5 million | 1–5 million | 1–5 million | 0.5–5 million | 6 million |
| Phenol–chloroform | Yes | Yes | Yes | None | None | None | None |
| Lysis buffer | SDS | SDS | SDS | CTAB or SDS | CTAB and CoHex | Proprietary | Proprietary |
| SPRI substrate | None | None | 3 mm glass beads | 3 mm glass beads | 3 mm glass beads | 4 mm glass beads | Nanobind disc |
| Precipitation reagents | Ethanol, ammonium acetate | Ethanol, ammonium acetate | Ethanol, ammonium acetate | Isopropanol, ammonium acetate | CoHex | Isopropanol, proprietary binding buffer | Isopropanol, proprietary binding buffer |
| DNA extraction time | 4 h | 4 h + overnight | 2 h | 1 h | 1 h | ∼30 min | 2 h |
| DNA resuspension time | 2 days | 2 days | min. overnight | min. 2 h | min. overnight | min. 1 h (standard overnight) | overnight |