Gene Expression Profiling Using 3 Tag Digital Approach

Massive parallel sequencing will become the method of choice for transcriptome profiling. Two protocols have been developed to quantify level of expressions: full-length RNA sequencing (RNA-SEQ) and 3′ tag digital gene expression (DGE). We have studied the performance of 3′ tag DGE profiling and used this protocol to compare the expression profiles of brain RNA to universal human reference RNA. This comparison highlighted that DGE is highly quantitative with excellent correlation of differential expression with quantitative real-time PCR. Our analysis also showed that when compared to microarray, one lane of 3′ DGE sequencing had wider dynamic range for transcriptome profiling and was able to detect expressed genes that are below the detection threshold of microarray. We conclude that 3′ tag DGE profiling is highly sensitive and reproducible for transcriptome profiling. It outperforms microarray platforms in detecting lower abundant transcripts.