Table 1 Comparison of different commercial kits for DNA extraction from rare cells
Cells | Kit | Protocol | 1.5 ml tube | 96 well-plate | Comments |
|---|---|---|---|---|---|
HCT116 Fresh | Qiagen QIAamp DNA Micro | Cell Protocol | 6–7 pg/cell (~100%) | 6-7pg/cell (~100%) | • Cell protocol performs well for a small amount of fresh cells, both in a tube or in a well-plate. |
|  |  |  |  |  | • Recommended for small amount of fresh/frozen cells. |
|  | Qiagen QIAamp DNA Micro | Cell Protocol | 0.1–0.5 pg/cell (<1%) | Not Tested | • Not optimal for fixed cells. |
|  |  | Tissue Protocol | 3–4 pg/cell (~50%) | 3–4 pg/cell (~50%) | • Tissue protocol performs well for a small amount of fixed cells. |
|  |  |  |  |  | • Selected for further optimization on fixed, permeabilized, immuno-stained cells. |
HCT116 Fixed | Qiagen GeneRead DNA FFPE | Standard Protocol | 2–3 pg/cell (~30%) | Not Tested | • Not optimal for fixed cells. |
|  |  |  |  |  | • Procedure is more complicated, with hazardous chemicals involved. |
|  | Zymo ZR Genomic DNA™ Tissue MicroPrep | Standard Protocol | 3–4 pg/cell (~50%) | 3–4 pg/cell (~50%) | • Could be used as a substitute for Qiagen Micro Kit. |
|  |  |  |  |  | • No further optimization has been performed. |
|  | Life technologies Arcturus® PicoPure® DNA Extraction | Standard Protocol | 3–4 pg/cell (~50%) | 0.5–1 pg/cell (<10%) | • Simple workflow with Applied Biosystems® Arcturus® LCM instruments. |
|  |  |  |  |  | • Small digestion volume causes evaporation during the incubation when using a 96 well-plate. |
