Single cell gene expression profiles are generated from cell suspensions containing up to 20.000 cells, by compartmentation of the cells in oil droplets. Within each droplet mRNA is converted to single strand cDNA based on a SMARTer based strategy. During first strand cDNA synthesis, a cell specific barcode and a molecular identifier (UMI) is incorporated at the 3’end of each transcript. Gene expression levels are estimated based on 3’UTR bulk sequencing the of the pooled cDNA populations of the individual cells. Each sequenced transcript will be assigned to a single cell based on the cell specific barcode.
