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Related Experiment Video

Updated: May 15, 2026

MISSION esiRNA for RNAi Screening in Mammalian Cells

MISSION esiRNA for RNAi Screening in Mammalian Cells

Published on: May 12, 2010

An analysis and validation pipeline for large-scale RNAi-based screens.

Michael Plank¹, Guang Hu, A Sofia Silva

¹Integrative Genomics of Ageing Group, Institute of Integrative Biology, University of Liverpool, Liverpool, UK.

Scientific Reports

|January 18, 2013

Summary

We developed a bioinformatics pipeline to prioritize candidate genes from RNA interference (RNAi) screens. While not identifying oxidative stress resistance genes, we confirmed Edd1 silencing impairs mouse embryonic stem cell growth.

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MISSION esiRNA for RNAi Screening in Mammalian Cells

MISSION esiRNA for RNAi Screening in Mammalian Cells

Published on: May 12, 2010

A Computational Pipeline for Intergenic/Intragenic Enhancer RNA Quantification in Mouse Embryonic Stem Cells

A Computational Pipeline for Intergenic/Intragenic Enhancer RNA Quantification in Mouse Embryonic Stem Cells

Published on: October 28, 2025

Area of Science:

Molecular Biology
Genetics
Bioinformatics

Background:

Large-scale RNA interference (RNAi) screens are crucial for identifying gene functions.
Effective prioritization and validation of candidate genes are essential for RNAi screen success.
Identifying genes involved in oxidative stress resistance is important for understanding cellular defense mechanisms.

Purpose of the Study:

To discover genes associated with oxidative stress resistance using a pooled shRNA screen in mouse embryonic stem cells (ESCs).
To develop and validate a bioinformatics pipeline for prioritizing candidate genes from large-scale RNAi screens.
To demonstrate the utility of the developed pipeline through a proof-of-concept study.

Main Methods:

Performed a large-scale pooled short hairpin RNA (shRNA) screen in mouse ESCs.
Developed a bioinformatics pipeline integrating effect sizes, functional enrichment, interaction networks, and gene expression data for candidate prioritization.
Utilized a fluorescence-based validation method comparing shRNA-expressing cells with internal control cells.

Main Results:

Identified several candidate genes from the initial screen, but did not pinpoint specific genes conferring oxidative stress resistance.
The bioinformatics pipeline successfully prioritized candidates.
Demonstrated a detrimental effect of Edd1 (Ectodermal dysplasia 1) gene silencing on ESC proliferation as a proof of concept.

Conclusions:

The developed bioinformatics pipeline offers a robust method for prioritizing candidate genes from large-scale RNAi screens.
The validation strategy using fluorescently tagged shRNAs allows detection of subtle gene effects.
While the primary goal of identifying oxidative stress resistance genes was not met, the study validates the pipeline's utility and highlights Edd1's role in ESC growth.