Droplet-based single cell RNAseq tools: a practical guide

Robert Salomon, Dominik Kaczorowski, Fatima Valdes-Mora, Robert E. Nordon, Adrian Neild, Nona Farbehi, Nenad Bartonicek, David Gallego-Ortega

Research output: Contribution to journalReview ArticleResearchpeer-review

57 Citations (Scopus)


Droplet based scRNA-seq systems such as Drop-seq, inDrop and Chromium 10X have been the catalyst for the wide adoption of high-throughput scRNA-seq technologies in the research laboratory. In order to understand the capabilities of these systems to deeply interrogate biology; here we provide a practical guide through all the steps involved in a typical scRNA-seq experiment. Through comparing and contrasting these three main droplet based systems (and their derivatives), we provide an overview of all critical considerations in obtaining high quality and biologically relevant data. We also discuss the limitations of these systems and how they fit into the emerging field of Genomic Cytometry.

Original languageEnglish
Pages (from-to)1706-1727
Number of pages22
JournalLab on a Chip
Issue number10
Publication statusPublished - 21 May 2019

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