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Pooled genetic perturbation screens with image-based phenotypes

Video protocol for performing optical pooled screens as described in the publication, “Pooled genetic perturbation screens with image-based phenotypes." Developed in the Blainey Lab at the Broad Institute of MIT and Harvard, this protocol uses in situ sequencing of cellular perturbation identities to enable high-throughput measurement of single-cell image phenotypes in pooled samples of genetic perturbations.

Computational resources and instructions for accessing example data are available on GitHub.


00:00 Introduction
3:09 Protocol overview
5:38 Sample preparation
7:10 In situ amplification and phenotype imaging
8:43 In situ sequencing-by-synthesis
10:16 Imaging overview
11:11 Ti-E and Micro-Manager imaging
15:12 Ti-2 and NIS Elements AR imaging
17:05 Data processing overview

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