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A method for performing high-throughput functional screening of genetic interactions and consequential phenotypes in single cells developed by researchers at UC San Francisco and the Broad Institute of MIT and Harvard. Their system uses CRISPR to cut DNA and perturb gene function and reads out the effects using single-cell RNA sequencing.

In 2016 the two initial Perturb-seq papers were published in Cell. Single-cell RNA sequencing is used to measure the effects of many CRISPR-based perturbations on large numbers of cells. To identify specific DNA changes or perturbations on individual cells within pooled experiments, cell barcoding is used on single cells from which transcriptional profiles were also acquired. Using droplet-based single-cell RNA sequencing, each cell has a gene expression profile associated one or more genetic perturbations.

Researchers of the paper led by the Broad Institute used CRISPR-Cas9 nucleases to cut DNA and inactivate genes for transcription factors (TFs), proteins that control the expression of genes involved in immune response in dendritic cells. They also inactivated genes for TFs and cell cycle regulator proteins in a cancer cell line.Lead author Jonathan S. Weissman is founder of KSQ therapeutics a company that uses CRISPR for genome screening.

The UCSF-led experiments used CRISPR-based transcriptional interference (CRISPRi) to repress genes in a cancer cell line to investigate errors in protein production that result from the cell sensing stress. Lead author Aviv Regev is a scientific advisor to ThermoFisher, Syros, and Driver.


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