A method of simultaneously analyzing RNA and DNA in a sample, the method comprising the steps of: (a) contacting the sample with a reverse primer from a first primer pair, the reverse primer from the first primer pair being directed to a target RNA region, and a reverse transcriptase to effect reverse transcription of the RNA into cDNA; (b) subsequently contacting the sample with: (i) a forward primer from the first primer pair, the forward primer from the first primer pair being directed to a target cDNA region, (ii) a reverse primer and a forward primer from a second primer pair, the reverse primer and forward primer from the second primer pair being directed to a target DNA region, and (iii) a DNA polymerase to simultaneously amplify the target cDNA region and the target DNA region; (c) (A) subjecting the sample from step (b) to a semi-nested PCR using the reverse primer in step (a) or the forward primer in step (b)(i), and a nested primer that binds within the amplified target cDNA region; and (B) subjecting the sample from step (b) to a nested PCR using a nested primer pair that binds within the amplified target DNA region;and (d) analyzing the amplified target cDNA region and the amplified target DNA region; wherein the sample is a single cell; and wherein the first primer pair comprises primers that span exon-exon boundaries or are separated by at least one intron on the corresponding DNA region; and wherein steps (a) and (b) are conducted in the same reaction mixture. (a) contacting the sample with a reverse primer from a first primer pair, the reverse primer from the first primer pair being directed to a target RNA region, and a reverse transcriptase to effect reverse transcription of the RNA into cDNA; (b) subsequently contacting the sample with: (i) a forward primer from the first primer pair, the forward primer from the first primer pair being directed to a target cDNA region, (ii) a reverse primer and a forward primer from a second primer pair, the reverse primer and forward primer from the second primer pair being directed to a target DNA region, and (iii) a DNA polymerase to simultaneously amplify the target cDNA region and the target DNA region; (i) a forward primer from the first primer pair, the forward primer from the first primer pair being directed to a target cDNA region, (ii) a reverse primer and a forward primer from a second primer pair, the reverse primer and forward primer from the second primer pair being directed to a target DNA region, and (iii) a DNA polymerase (c) (A) subjecting the sample from step (b) to a semi-nested PCR using the reverse primer in step (a) or the forward primer in step (b)(i), and a nested primer that binds within the amplified target cDNA region; and (B) subjecting the sample from step (b) to a nested PCR using a nested primer pair that binds within the amplified target DNA region;and (A) subjecting the sample from step (b) to a semi-nested PCR using the reverse primer in step (a) or the forward primer in step (b)(i), and a nested primer that binds within the amplified target cDNA region; and (B) subjecting the sample from step (b) to a nested PCR using a nested primer pair that binds within the amplified target DNA region;and (d) analyzing the amplified target cDNA region and the amplified target DNA region; <EOS>