In 2012, our lab published CEL-Seq, a method for single-cell RNA-Seq. The method is highly-multiplexed, uses in vitro transcription (IVT) to amplify, and has become one of the best methods for single-cell RNA-Seq. We believe it is actually THE best method!
We have recently developed CEL-Seq2 which has three times better sensitivity than the original, and is also cheaper and faster. Our recent paper in Genome Biology contains the full protocol.
Kelly Rae Chi also mentions CEL-Seq in her review for The Scientist on single-cell RNA-Seq methods.
In March 2017, the Institute for Computational Medicine held a workshop at NYU School of Medicine about CEL-Seq2..