An integrated 5'- and 3'-end RNA sequencing platform for high-throughput transcriptome quantitation and annotation
RNA-Seq provides an effective way to annotate and measure the transcriptome, but the combination of cost, analysis and end-mapping challenges has limited its adoption for high-throughput quantitation and annotation. Here, we present an integrated experimental and computational suite for transcriptome annotation and quantitation based on the sequencing of mRNA ends. It consists of: a novel, simple, one-step, strategy 5' RNA-Seq; an optimized library construction method for strand-specific 3' RNA-seq that reduces costs and time; and a complete computational analysis toolkit. We demonstrate the power and versatility of our approach to study the transcriptome of LPS stimulation in mouse dendritic cells, promoter structure of the TCRb locus in mouse T cells, and gene expression in circadian cycles in Drosophila. Our platform provides a comprehensive solution for high-throughput, cost-effective transcriptome quantification and end annotation. Overall design: A study of 5' and 3' end RNA sequencing methods