dsCAGE - direct cDNA CAGE for paired-end patterned flowcell sequencing.

CAGE is a technique that has proven to be very insightful over the years to assess the 5'-end of RNA transcripts of both coding and non-coding genes. Here we describe its use on the newest Illumina patterned flowcell technology with added dual indexes, using mouse and human samples. We detail the procedure for sequencing and semi-automated data analysis. This protocol keeps CAGE relevant for the determination of transcription start sites and enhancers on the ever evolving Illumina sequencing platforms.