Table 3.
Summary of the procedural steps used by the different FFPE-ChIP techniques and kits for chromatin extraction.
| PAT-ChIP | FiT-seq | EPAT-ChIP | Chrom-EX PE | FiTAc-seq | RCRA ChIP-seq | ChIP-IT FFPE Chromatin Preparation II | truChIP FFPE | |
|---|---|---|---|---|---|---|---|---|
| MNase digestion | 1 min at 37 °C with 0.1 U MNase/µg of chromatin | None | None | None | None | None | None | None |
| Prot. K treatment | None | 40 ng/µL for 5–10 min | None | None | None | None | None | 80 ng/μL for 10 min at 40 °C |
| Heating (LRC) | None | None | 1 h at 80 °C with 0.05% Tween-20 | 16 h at 65 °C with 0.5% Triton-X 100 and 0.1% sodium deoxycholate | 16 h at 65 °C with 1% SDS | 60 min at 65 °C followed by 30 min at 90 °C in 0.1% SDS | 1 h at 50 °C in “ChIP buffer” | None |
| Lysis (II) | None | None | None | 10 min in ice with 0.5% IGEPAL | None | None | None | None |
| Sonication (paraffin emulsification) | None | None | None | None | None | None | None | Covaris M220, 5 min at 20 °C (duty factor 20%, peak incident 75 W, 200 cycles per burst) |
| Sonication (chromatin extraction) | Probe sonicator, 3 × 30 s at 85% amplitude in 0.1% SDS | Covaris E210, 40 min in 0.1% SDS (duty factor 20%, intensity 8, 200 cycles per burst) | Probe sonicator, 3 × 30 s at 40% amplitude in 0.1% SDS | Bioruptor Twin (UCD-400), 3 × (30 × 30 s) in 1% Triton X-100, 0.1% sodium deoxycholate, 0.05% SDS | Covaris E220 5 min in 1% SDS (duty factor 5%, peak incident 105 W, 200 cycles per burst) | Bioruptor II, 60 × 30 s in 1% Triton-X 100, 0.5% IGEPAL (BM Equipment) | Probe sonicator, 40 × 30 s at 42% amplitude in “ChIP buffer” | Covaris M220, 10–30 min at 7 °C (duty factor 15%, peak incident 75 W, 200 cycles per burst) after the addition of “shearing buffer” |
Conditions are reported only if published or described in kit datasheets. Buffer composition: in the absence of other relevant features, only the concentrations of detergents and salts are reported.