Abstract: Provided herein are methods for detection of a target nucleic acid from a single cell. Preferred embodiments of the method include selecting one or more target nucleic acid sequence of interest in an individual cell, where the target nucleic acid sequence is typically complementary to cellular DNA, including a genomic DNA, and an RNA in a cell. A cell sample is provided, and in preferred embodiments the sample is from a single cell. The cell is lysed and in a single reaction both DNA and RNA can be detected without sub-dividing the sample. This can be accomplished by providing nucleic acid amplification primer sets complementary to one or more target nucleic acid, and in particular primer sets that selectively amplify particular target nucleic acids or amplicons in an amplification reaction. Also provided are methods of primer design for these methods and apparatus and system used to perform the methods.