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Advances in single cell analysis offer multiple techniques for assessing DNA and RNA from cells, yet there lacks a simple tool to assess DNA and RNA from the same cell at whole-transcriptome and whole-genome depts. Using a simple three step approach in conjunction with the CellRaft Array: immobilization, lysis, and separation, this study found that DNA and RNA extracted from single cells is suitable for downstream, sequencing-based applications. The CellRaft Array provided thousands of single cells to be observed, selected, and isolated into PCR tubes using the magnetic collection wand. Once in the tube, lysis buffer was introduced to release cytoplasm into the aqueous phase. The supernatant containing RNA was aspirated leaving the DNA-containing nucleus attached to the CellRaft in the tube. DNA and RNA are physically separated from each other and can be processed or stored at -80°C until needed. This method can serve as a tool for simultaneous complex analysis of the genome and transcriptome, providing necessary information on the relationship between somatic mutations and the regulation of gene expression.