Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Accurate quantification of CRISPR effects in pooled FACS screens using Waterbear

ABSTRACT: Accurate quantification of CRISPR effects in pooled FACS screens using Waterbear

PROVIDER: PRJNA1015217 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Accurate quantification of CRISPR effects in pooled FACS screens using Waterbear

Project description:CRISPR screens are powerful tools to identify key genes that underlie biological processes. One important type of screen uses fluorescence activated cell sorting (FACS) to sort perturbed cells into bins based on the expression level of a marker gene, followed by guide RNA (gRNA) sequencing. Analysis of these data presents multiple statistical challenges due to multiple factors including the discrete nature of the bins and typically small numbers of replicate experiments. To address these challenges, we developed a robust and powerful Bayesian random effects model and software package called Waterbear. Furthermore, we used Waterbear to explore how various experimental design parameters affect statistical power to establish principled guidelines for future screens. Finally, we experimentally validated our model findings that, when using Waterbear for analysis, high power is maintained even at low coverage and a high multiplicity of infection. We anticipate that Waterbear will be of broad utility for analyzing FACS-based CRISPR screens.

2025-10-01 | GSE242880 | GEO

A model for accurate quantification of CRISPR effects in pooled FACS screens.

Project description:CRISPR screens are powerful tools to identify key genes that underlie biological processes. One important type of screen uses fluorescence activated cell sorting (FACS) to sort perturbed cells into bins based on the expression level of marker genes, followed by guide RNA (gRNA) sequencing. Analysis of these data presents several statistical challenges due to multiple factors including the discrete nature of the bins and typically small numbers of replicate experiments. To address these challenges, we developed a robust and powerful Bayesian random effects model and software package called Waterbear. Furthermore, we used Waterbear to explore how various experimental design parameters affect statistical power to establish principled guidelines for future screens. Finally, we experimentally validated our experimental design model findings that, when using Waterbear for analysis, high power is maintained even at low cell coverage and a high multiplicity of infection. We anticipate that Waterbear will be of broad utility for analyzing FACS-based CRISPR screens.

| S-EPMC11213010 | biostudies-literature

Assaying for RNA abundance and protein phosphorylation in pooled CRISPR screens

Project description:Pooled CRISPR screens are a powerful tool to identify regulators of a biological process, but have been limited to phenotypes that affect viability or can be monitored with fluorescent protein reporters. We evaluate two additional strategies for phenotypic enrichment based on quantification of RNA using a Flow-FISH assay or protein phosphorylation through intracellular phospho-staining. These tools will greatly expand the applicability of CRISPR screens since they increase the number of possible molecular phenotypes and assay designs.

2023-02-09 | GSE145063 | GEO

Pooled CRISPR screens in human intestinal organoids [CRISPR screens]

Project description:Pooled CRISPR screens in human intestinal organoids [CRISPR screens]

| PRJNA608420 | ENA

Pooled CRISPR screens in human macrophages

Project description:Pooled CRISPR screens in human macrophages

| PRJNA893203 | ENA

Multiplexed Perturbation Enables Scalable Pooled Screens

Project description:Multiplexed Perturbation Enables Scalable Pooled Screens

| PRJNA1290110 | ENA

Pooled CRISPR screens in human intestinal organoids

Project description:Pooled CRISPR screens in human intestinal organoids

| PRJNA608374 | ENA

Multiplexed Perturbation Enables Scalable Pooled Screens

Project description:CRISPR-based genetic perturbation screens have revolutionized the ability to link genes to cellular phenotypes with unprecedented precision and scale. However, conventional pooled CRISPR screens require large cell numbers to achieve adequate sgRNA representation, posing technical and financial challenges. Here, we investigate the impact of multiplexed sgRNA delivery via high multiplicity of infection (MOI) in pooled CRISPR interference (CRISPRi) screens as a strategy to enhance screening efficiency while reducing cell numbers. We systematically evaluate screen performance across varying MOIs, assessing the effects of multiplexing on knockdown efficiency, sgRNA representation, and collision rates. Our data demonstrate that sgRNA multiplexing (MOI 2.5-10) can maintain screen performance while enabling significant reductions in cell requirements. We further apply these optimized conditions to conduct a genome-wide CRISPR screen for regulators of intracellular adhesion molecule ICAM-1, successfully identifying novel candidates using as few as half a million cells. This study provides a framework for adopting multiplexed sgRNA strategies to streamline CRISPR screening applications in resource-limited settings.

2026-01-16 | GSE302335 | GEO

Pooled CRISPR screens in human intestinal organoids [ATAC-seq]

Project description:Pooled CRISPR screens in human intestinal organoids [ATAC-seq]

| PRJNA608811 | ENA

Pooled CRISPR screens in human intestinal organoids [CUT&RUN]

Project description:Pooled CRISPR screens in human intestinal organoids [CUT&RUN]

| PRJNA608810 | ENA