Targeted single-cell RNA sequencing enables genome-scale CRISPR screens

CRISPR screening has become the prime discovery tool in modern biomedical research and drug discovery. At the same time, most screens conducted today rely on rather simplistic read-outs.

 

At Aelian, we use the CROP-seq (CRISPR droplet sequencing) workflow developed by Aelian co-founder Christoph Bock to combine CRISPR screening with single-cell transcriptomics, leveraging two transformative technologies to enable genetic screening for complex phenotypes. Our powerful approach has broad applications in identifying novel drug targets or elucidating unknown mechanisms of actions of drugs.

 

Currently, most single-cell RNA sequencing platforms utilize an unbiased sequencing approach. While powerful, it typically delivers shallow sequencing data for each single cell. At Aelian, we combine CRISPR perturbation with targeted single-cell RNA sequencing using the BD Rhapsody workflow, coupled with Illumina sequencing readout, to focus sequencing resources on the most informative transcripts. The data we gathered suggest that targeted sequencing leads to a reduction in cost as cells can be sequenced at 10x reduced depth. At the same time, the signal-to-noise ratio improves significantly, thus enhancing the dynamic range of CROP-seq screens.

 

Overall, advances presented here will pave the way towards genome-scale single-cell CRISPR screens.

 

In addition, this webinar will see Dr. Pawel Zajac presenting the latest Illumina news and Dr. Wieland Keilholz introducing the BD Rhapsody single-cell analysis system.

 

Learning Objectives