One of my favorite papers is by a group that was able to quantify the transcriptome of individual cells that comprised a complex tissue, originally. Drop-Seq analysis was performed- cell identification and transcript quantification were achieved through the incorporation of common cellular barcodes and Unique Molecular Identifiers into the PCR primers, respectively.

Macosko, E. Z., Basu, A., Satija, R., Nemesh, J., Shekhar, K., Goldman, M., Tirosh, I., Bialas, A. R., Kamitaki, N., Martersteck, E. M., Trombetta, J. J., Weitz, D. A., Sanes, J. R., Shalek, A. K., Regev, A., and McCarroll, S. A. (2015) Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets, Cell 161 , 1202-1214.