This protocol describes the extraction, fractionation, and recovery of cytoplasmic nucleic acids (e.g., cytoplasmic RNA) versus nucleic acids in the cell nucleus (including genomic DNA, gDNA) from single cells with a microfluidic system. The method enables independent, sequence-specific analyses of these critical markers (Kuriyama et al., 2015). The system uses a microfluidic chip with a simple geometry and four end-channel electrodes, and completes the entire process in less than 5 min, including lysis, purification, fractionation, and delivery to two output reservoirs: One for the nucleus (including gDNA and nuclear RNA) and one for cytoplasmic RNA. Each reservoir then contains high quality and purity aliquots with no measurable cross-contamination of cytoplasmic RNA versus nucleic acids in nucleus. As described here, our protocol focuses on the analysis of cytoplasmic RNA versus gDNA from the nucleus. We have tested this protocol with mouse and human cells but not with walled cells such as plant cells.
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