VIPerturb-seq: Genome-Wide CRISPR Screens at Single-Cell Resolution

Genome-wide CRISPR screening has long meant trading resolution for scale. Learn how a probe-based, fixed-cell Perturb-seq workflow eliminates the trade-off and makes single-cell, whole-genome screens practical for routine use.

Register Free: https://www.pharmtech.com/pt_w/CRISPR-Screens

Event Overview:

Pooled CRISPR screening with a single-cell readout enables systematic mapping of genetic perturbations to molecular phenotypes, but cost and throughput remain substantial barriers to routine genome-wide experiments. This session introduces VIPerturb-seq, a method developed in the Satija Lab that enables whole-genome CRISPR screens on 10x Genomics Flex Apex chemistry — combining probe-based detection of genome-wide CRISPR libraries in fixed cells with scalable single-cell profiling. The approach supports both unbiased screens using combinatorial indexing and phenotypic enrichment of cells with molecular features of interest, allowing researchers to focus sequencing on informative perturbations without preselecting candidate genes.

Results from three genome-wide CRISPRi screens will illustrate these complementary strategies: an unbiased screen profiling 880,000 cells performed in a single afternoon, a screen using intracellular protein enrichment to identify regulators of vimentin, and a new screen using RNA-based enrichment to identify regulators of RNA surveillance. This session will also cover the practical considerations for library design, phenotypic enrichment, and experiment scaling, and show how Flex Apex with VIPerturb-seq makes genome-wide, single-cell screening accessible both to large-scale data generation platforms building virtual cell models and to biopharma laboratories running target discovery programs.

Key Learning Objectives:

• Understand how probe-based detection enables genome-wide Perturb-seq
• Compare unbiased versus phenotypically enriched screen designs
• Assess cost, throughput, and sensitivity trade-offs at genome scale
• Apply fixed-cell workflows to fragile, enriched, and in vivo samples

Who Should Attend:

• Scientists, senior scientists, and principal scientists in functional genomics, target discovery, and genomic medicine
• Group leaders and principal investigators; directors and heads of target discovery, platform technology, and computational biology; single-cell and genomics core facility directors

Speakers:

Lauren Neves, PhD
Science and Technology Advisor
10x Genomics

Lauren Neves, PhD, is the science and technology advisor at 10x Genomics, supporting biopharma customers in Northern California, Los Angeles, and Washington. Neves originally joined 10x in 2022 as a field application scientist, bringing 10 years of extensive molecular biology knowledge across academia and life science tool providers.

Rahul Satija, PhD
Core Faculty Member
New York Genome Center

Rahul Satija, PhD, is a core faculty member at the New York Genome Center (NYGC), with a joint appointment as professor at the Center for Genomics and Systems Biology at New York University. Prior to joining the NYGC, Satija was a postdoctoral researcher at the Broad Institute of Harvard and MIT, where he developed new methods for single-cell analysis. The Satija Lab focuses on developing computational and experimental methods to sequence and interpret the molecular contents of a single cell. His lab applies single-cell genomics to understand the causes and consequences of cell-to-cell variation, with a particular focus on immune regulation and early development. Satija is a recipient of the NIH New Innovator Award and, in 2020, was selected to direct an NIH Center for Excellence in Genomic Science.

Register Free: https://www.pharmtech.com/pt_w/CRISPR-Screens