For the past several decades, due to technical limitations, the field of transcriptomics has focused on population\u2010level measurements that can mask significant differences between individual cells. With the advent of single\u2010cell RNA\u2010Seq, it is now possible to profile the responses of individual cells at unprecedented depth and thereby uncover, transcriptome\u2010wide, the heterogeneity that exists within these populations. This unit describes a method that merges several important technologies to produce, in high\u2010throughput, single\u2010cell RNA\u2010Seq libraries. Complementary DNA (cDNA) is made from full\u2010length mRNA transcripts using a reverse transcriptase that has terminal transferase activity. This, when combined with a second \u201ctemplate\u2010switch\u201d primer, allows for cDNAs to be constructed that have two universal priming sequences. Following preamplification from these common sequences, Nextera XT is used to prepare a pool of 96 uniquely indexed samples ready for Illumina sequencing.\u00a0Curr. Protoc. Mol. Biol. 107:4.22.1\u20104.22.17. \u00a9 2014 by John Wiley & Sons, Inc.