Nucleic acid extraction from formalin-fixed paraffin-embedded cancer cell line samples: a trade off between quantity and quality?

Table 1 Summary of the seven off the shelf nucleic extraction kits evaluated in this study, including the key differences between each method

Extraction kit	Manufacturer	Extracted Material	Input tissue amount	Elution Volume	Purification Method	Level of automation	Proteinase K digestion	DNase I digestion	Geometric mean Yield (ng)
RNeasy FFPE	Qiagen	RNA	Up to 40 μm	30 μl	Silica Column	Manual	15 min at 56 °C, 15 min at 80 °C	15 min at room temperature in the cell lysate	398.0
Arcturus Paradise plus RNA extraction and isolation	Life technologies	RNA	Up to 40 μm	12 μl	Silica Column	Manual	5 h at 37 °C	20 min at room temperature on the column	197.0
Maxwell 16 LEV RNA FFPE Kit	Promega	RNA	Up to 10 μm	50 μl	Paramagnetic beads	Automated	15 min at 56 °C, 60 min at 80 °C	15 min at room temperature in the cell lysate	231.5
AllPrep DNA/RNA FFPE	Qiagen	RNA & DNA	Up to 40 μm	RNA 30 μl DNA 50 μl	Silica Column	Manual	15 min at 56 °C	15 min at room temperature on the column	RNA 267.7 DNA 10.1
Arcturus PicoPure DNA extraction kit	Life technologies	DNA	1.5–2.0 μg tissue	150 μl	Single tube extraction	Manual	24 h at 65 °C (lyophilised before use)	N/A	172.6
QIAmp DNA FFPE tissue	Qiagen	DNA	Up to 80 μm	50 μl	Silica Column	Manual	60 min at 56 °C, 60 min at 80 °C	N/A	40.9
Maxwell 16 FFPE Tissue LEV DNA Purification Kit	Promega	DNA	Up to 50 μm	50 μl	Paramagnetic beads	Automated	Overnight at 70 °C	N/A	88.3

ISSN: 1472-6890