Gene Expression Profiling Using 3 Tag Digital Approach
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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.