QuestionsCategory: Single-Cell RNA-SeqDroplet-based (e.g. 10x Genomics) or plated-based (e.g. Smart-Seq)? When should one be considered over the other asked 2 years ago

What is the difference between high throughput single cell methods like droplet-barcoding (like 10x Genomics Chromium) and plate-based methods (ike ‘Smart-Seq”)? Which is more sensitive? What is the comparative cost of each? 

1 Answers answered 2 years ago

A key difference between Smart -Seq2 and the 10x Chromium protocol lies in the way the RNA is processed to cDNA. Smart-seq2 captures the full-length mRNA, although with significant 3′ bias because of oligo dT primers used during cDNA generation, while the 10x protocol is based on a 3′-tag sequencing method  Accordingly, it is important to consider the aim of the study when selecting a method for single-cell RNA-seq. For example, full-length capture is needed for studies concerned with isoforms or gene fusions, while 3′-tag methods can capture more cells and thus give an aggregate view of the transcriptional heterogeneity of a given cell population.