A sensitive transcriptome analysis method

We have developed a gene expression profiling method called 'High coverage expression profiling' (HiCEP) analysis. The method requires no sequence information and so is applicable even to eukaryotes for which there is no genome information available. By making improvements to the selective PCR technique we have reduced the rate of false-positive peaks to approximately 5% and then the number of peaks including overlapping peaks was decreased drastically. This enables us to determine the relationship between peaks and original transcripts unequivocally, and will make it practical to prepare a database for all peaks. The precise selection also enables us to easily clone peaks of interest and predict the corresponding gene for each peak. The procedure is highly reproducible and sensitive enough to detect even a 1.2-fold difference in gene expression. Most importantly, the low false-positive rate enabled us to analyze gene expression with wide coverage by means of 4-nucleotide recognition restriction enzymes for the finger printing of mRNAs. The method detects 70-80% of all transcripts, including non-coding transcripts, unknown and known genes