Highly parallel genome wide expression profiling is a drop-seq method to analyze mRNA expression in thousands of individual cells. It works by encapsulating cells in tiny droplets for parallel analysis, droplets have been used as tiny reaction chambers for PCR and reverse transcription. To retain the molecular memory of the identity of the cells from which each mRNA transcript was isolated it was used a molecular barcoding strategy.

Steps (1) prepare a single-cell suspension from a tissue; (2) co-encapsulate each cell with a distinctly barcoded microparticle (bead) in a nanoliter-scale droplet; (3) lyse cells after they have been isolated in droplets; (4) capture a cell's mRNAs on its companion microparticle, forming STAMPs (single-cell transcriptomes attached to microparticles); (5) reverse-transcribe, amplify, and sequence thousands of STAMPs in one reaction; and (6) use the STAMP barcodes to infer each transcript's cell of origin.