The C1 Single-Cell Auto Prep system now features an mRNA sequencing application that can give researchers an end-to-end workflow for transcriptome analysis of 96 single cells. mRNA Seq kits and integrated fluidic circuits enable the parallel processing of up to 96 single-cell cDNA libraries for quantitation of mRNA expression on Illumina sequencers. This sequencing workflow was created for high-throughput single-cell analysis. The application enables measurement of expression levels of genes, alleles, and spliced variants, comparison of expression profiles between individual cells and populations, mapping of transcription initiation sites, characterization of alternate splicing patterns, evaluation of post-transcriptional activity, and discovery of new transcripts and gene fusions.