A method for analyzing the qualitative and quantitative aspects of gene expression: A transcriptional profile revealed for HeLa cells

A number of strategies have been devised by which differentially expressed genes in different cell types or tissues can be identified. We here report an efficient method to analyze the qualitative and quantitative aspects of transcripts and to construct an extensive gene expression profile in any kind of cell or tissue of interest. This method enables us to analyze the composition of mRNA species, reflecting gene activities, by measuring the frequency of appearance of concatamerized 17mer cDNA mini-fragments, which are proportional to the abundance of mRNA. As compared with a related method previously described by others, we can analyze ~ 3-4 bp longer cDNA fragments derived from amounts of total RNA as small as 1 μg. Using this technique we examined 10 100 cDNA mini-fragments from HeLa cells and constructed a gene expression profile consisting of 3665 genes. This method should thus provide an overall indication of gene activities and a rational means for monitoring gene fluctuation in different cells or tissues at different stages of development, in normal and disease states.