Evaluating capture sequence performance for single-cell CRISPR activation experiments

The combination of single-cell RNA sequencing with CRISPR inhibition/activation provides a high-throughput approach to simultaneously study the effects of hundreds if not thousands of gene perturbations in a single experiment. One recent development in CRISPR-based single-cell techniques introduces a feature barcoding technology that allows for the simultaneous capture of mRNA and guide RNA (gRNA) from the same cell. This is achieved by introducing a capture sequence, whose complement can be incorporated into each gRNA and that can be used to amplify these features prior to sequencing. However, because the technology is in its infancy, there is little information available on how such experimental parameters can be optimized. To overcome this, researchers at Duke-NUS Medical School varied the capture sequence, capture sequence position, and gRNA backbone to identify an optimal gRNA scaffold for CRISPR activation gene perturbation studies. The researchers provide a report on their screening approach along with their observations and recommendations for future use.

Choo XY, Lim YM, Katwadi K, Yap L, Tryggvason K, Sun AX, Li S, Handoko L, Ouyang JF, Rackham OJL. (2021) Evaluating Capture Sequence Performance for Single-Cell CRISPR Activation Experiments. ACS Synth Biol [Epub ahead of print]. [article]

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