Quantitative RNA Analysis Using RNA-Seq.

High-throughput sequencing of cDNA copies of mRNA (RNA-seq) provides a digital readout of mRNA levels over several orders of magnitude, as well as mapping the transcripts to the nucleotide level. Here we describe two different RNA-seq approaches, including one that exploits the 39-nucleotide mini-exon or spliced leader (SL) sequence found at the 5' end of all Leishmania (and other trypanosomatid) mRNAs.