RNA-Seq is a powerful tool for studying various aspects of RNA biology, including expression levels, alternative splicing, RNA editing, and gene discovery. Though RNA-Seq has long been in use, robust and easy methods for generating strand-specific libraries and libraries from total RNA samples have not been commercially available. The new Illumina Tru-Seq Strand-specific Total RNA-Seq kits facilitate the generation of high quality libraries via a simple, rapid, and familiar workflow. I will present modENCODE data generated using these new kits and compare the results to those generated from libraries prepared using previous Illumina RNA-Seq kits and the same RNA samples. Specifically, I will discuss the degree of strandedness, evenness of coverage, and discovery of transcribed regions not identified using poly(A)-selected RNA-Seq libraries.