High-throughput analysis of total RNA expression profiles by capillary gel electrophoresis

We studied the expression profiles of total RNA in three types of human tissues. Reverse transcription was performed on total RNA samples extracted from kidney, normal breast, and breast tumor. Then, fluorophor-labeled cDNAs were synthesized by using random hexamers as primers for analysis by capillary gel electrophoresis. By overlaying the electropherograms and by performing multivariate analysis, we found that the RNA patterns were significantly different among the tissue samples. The protocol utilizes only submicroliter volumes of PCR products and is compatible with multiple capillary DNA sequencing instruments. These CE-based RNA patterns provide an alternative to RNA microarrays for expression profiling for understanding the molecular basis of disease.