Single cell RNA sequencing with Fluidigm vs Drop-seq?

Question

[halo22]

Our group is interested in conducting a single cell RNA-sequencing experiment, currently we have two choices to go with the Fluidigm (C1) and Drop-Seq. I would like to get recommendations from you all about the quality of sequencing and the ease data analysis with these two systems.

Answer 1

[Charles Plessy]

Droplet-based platforms offer a higher throughput, meaning a lower cost per cell. The Fluidigm platform has a lower throughput, but gives the possibility to take a picture of the cells before lysis, which not only allows for ensuring that there was really one single cell (not zero, nor two, nor debris), but also allows for more sophisticated experimental designs, for example if your cells express transgenes, like in our single-cell RNA-seq analysis of the cell cycle.