AllPrep DNA/RNA FFPE Kit

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Publication protocol

Nucleic acid isolation and quantification: We compared the performance of eight RNA and eight DNA extraction protocols (from 14 commercial kits) using 0.68 mm3 of the homogenized tissue. For each kit, the manufacturer’s protocols were followed (see Table 1 for more details). Generally, the extraction process involved rehydration of the homogenized tissue, followed by protease digestion, binding to a solid substrate, washing, and elution, with variations specific to each kit/protocol. Three tech- nical replicates were performed for each extraction kit.
Two of the kits tested, RecAll (ThermoFisher Scientific) and AllPrep (Qiagen), are dual- extraction kits, which permit extraction of RNA followed by DNA from the same input tissue. For these two kits, after the homogenized tissue was treated with Proteinase K and then centri- fuged, the resulting tissue pellets were used as input for DNA extraction, while the supernatant was used for RNA extraction.
For each extraction, the DNA and RNA yields were quantified on a Qubit 3.0 Fluorometer (ThermoFisher Scientific), using the dsDNA HS (High Sensitivity) and RNA BR (Broad- Range) Assay kits, respectively. The purity of the extracted nucleic acids was assessed by the A260/280 and A260/230 absorbance ratios obtained using a NanoDrop spectrophotometer.

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