Single-cell Genomics – Are We There Yet

Vladimir Benes
Malte Paulsen, Diana Ordonez, Bianka Baying, Dinko Pavlinic, Jonathan Landry, Vladimir Benes
EMBL, Germany, Flow Cytometry Core Facility, Genomics Core Facility

The advent of single cell sequencing technologies created a very productive and collaborative environment for genomics and flow cytometric methods in the last five years. Flow Cytometry by nature was in the past the best method to analyse quickly thousands, if not millions, of cells for their expression of proteins, peptides or analysing the metabolic state with single cell resolution. Sequencing technologies have closed the gaps improving the quality and general robustness of sequencing DNA and RNA from single cells. This finally let to the development of multiple different, easy to use approaches in single cell generation and subsequent sequencing methods. Single cell sorting by FACS or Fluidigm C1 capture paired with sensitive library preparation methods paved the way. Nowadays, complete kit-solutions from 10xGenomics and their likes have rendered the initial resistance – or better put the initial need for intense technical skill development – to enter this method field almost to zero. Automation of analysis processes and kit-based scientific methods are probably the biggest driver for the high pace science that we are currently enjoying, yet at the same time it is most probably also responsible for the increased appearance of methodically poorly designed studies. We see a steep increase in studies that involve to a significant level single cell sequencing data. What strikes us is the apparent complacency of how authors set up their experiments. Studies with poor methodology are not rare in scientific literature and sadly, to some extent repeat the qPCR story.

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