Labchip gx gxii microfluidic system

Cell line DNA (from around three millions of cells) was extracted using QIAamp® DNA Mini Kit, while DNA from FFPE samples (patient’s sample or Multiplex FFPE Reference Standards) was isolated with QIAamp® DNA FFPE Tissue Kit (QIAGEN, Les Ulis, France) according to the manufacturer’s instructions. DNA from cell lines and DNA from FFPE samples were eluted in 200 μL or 100 μL of elution buffer, respectively.
Cell-free DNA [12 (link)] (cfDNA) was extracted from plasma samples using QIAmp® Circulating Nucleic Acid Kit (QIAGEN, Les Ulis, France) according to the manufacturer’s instructions, and resuspended into 50 μL of elution buffer.
The DNA quantity has been measured by Qubit® 2.0 Fluorometer (Qubit® dsDNA BR Assay kit for DNA from cell lines and HS Assay kit for cfDNA—Life Technologies-Thermo Fisher Scientific, Saint Aubin, France) [32 (link)].
All DNA used in the study were kept at -20°C before use.
Genomic wild-type and mutated DNA were fragmented with S220 Focused-Ultrasonicator sonicator (Covaris, Woburn, MA) to mean sizes of 600–800 base-pairs (bp). DNA sizes have been verified by LabChip® GX/GXII Microfluidic system (Perkin-Elmer, Villebon-sur-Yvette, France) using DNA assay 5K reagent kit (Perkin-Elmer, Villebon-sur-Yvette, France).

DNA was extracted from two cell lines SW620 (mutated KRAS c.35G>T, p.G12V) and LoVo cell lines (mutated c.38G>A, p.G13D) using the QIAamp DNA Blood Mini Kit (QIAGEN) according to the manufacturer's instructions and eluted into 200 μl of Tris 10 mM/pH 8 before storage at −20°C.
The extracted DNA was fragmented by sonication (S220 Covaris Focused-Ultrasonicator sonicator) to obtain fragments ranging from 50 to 700 bp. The experimental parameters are described in Supplementary Table 2. The size distribution of fragmented DNA was confirmed by the miniaturized electrophoresis Caliper system, LabChip® GX/GXII Microfluidic system (Perkin-Elmer) using DNA assay 5K reagent kit (Perkin-Elmer) (see Supplementary Figure 2 for size distribution).