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Related Concept Videos

CRISPR/Cas9 Genome Editing01:28

CRISPR/Cas9 Genome Editing

99
The CRISPR-Cas system serves as a bacterial defense mechanism against invading genetic elements such as viruses and plasmids, forming the foundation for its adaptation as a powerful genome-editing tool. Originally discovered in prokaryotes, this system has been repurposed to revolutionize genetic engineering across a wide range of organisms, including plants, animals, and humans. The core component, Cas9, is an endonuclease derived from Streptococcus pyogenes, capable of introducing...
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CRISPR and crRNAs02:53

CRISPR and crRNAs

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Bacteria and archaea are susceptible to viral infections just like eukaryotes; therefore, they have developed a unique adaptive immune system to protect themselves. Clustered regularly interspaced short palindromic repeats and CRISPR-associated proteins (CRISPR-Cas) are present in more than 45% of known bacteria and 90% of known archaea.
The CRISPR-Cas system stores a copy of foreign DNA in the host genome and uses it to identify the foreign DNA upon reinfection. CRISPR-Cas has three different...
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CRISPR01:59

CRISPR

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Genome editing technologies allow scientists to modify an organism’s DNA via the addition, removal, or rearrangement of genetic material at specific genomic locations. These types of techniques could potentially be used to cure genetic disorders such as hemophilia and sickle cell anemia. One popular and widely used DNA-editing research tool that could lead to safe and effective cures for genetic disorders is the CRISPR-Cas9 system. CRISPR-Cas9 stands for Clustered Regularly Interspaced...
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Related Experiment Video

Updated: Aug 9, 2025

Pooled CRISPR-Based Genetic Screens in Mammalian Cells
09:05

Pooled CRISPR-Based Genetic Screens in Mammalian Cells

Published on: September 4, 2019

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An interactive web application for processing, correcting, and visualizing genome-wide pooled CRISPR-Cas9 screens.

Alessandro Vinceti1, Riccardo Roberto De Lucia1, Paolo Cremaschi1

  • 1Computational Biology Research Centre, Human Technopole, Viale Rita Levi-Montalcini, 1, 20157 Milano, Italy.

Cell Reports Methods
|February 23, 2023
PubMed
Summary
This summary is machine-generated.

CRISPRcleanR web application simplifies CRISPR-Cas9 screen analysis by reducing false positives from amplified genomic regions. This tool enhances the accuracy of identifying essential genes, improving genetic dependency studies.

Keywords:
CRISPR-Cas9 screensbias correctioncancer dependencycopy numberdata explorationdata visualizationgene essentialitypost-genomic dataunsupervised analysisweb application

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Area of Science:

  • Genomics
  • Bioinformatics
  • CRISPR Technology

Background:

  • Pooled CRISPR-Cas9 screens are powerful for identifying essential genes but suffer from high false-positive rates.
  • Copy-number-amplified genomic regions often lead to inaccurate essentiality calls in CRISPR screens.
  • Existing computational tools require significant bioinformatics expertise.

Purpose of the Study:

  • To introduce CRISPRcleanR, a user-friendly web application for analyzing pooled CRISPR-Cas9 screening data.
  • To provide an accessible platform for detecting and correcting biases in CRISPR screens, particularly those caused by genomic amplifications.
  • To improve the accuracy and sensitivity of essential gene identification in CRISPR screens.

Main Methods:

  • Development of a web application interface for the existing CRISPRcleanR computational method.
  • Implementation of an unsupervised algorithm to detect and correct biased CRISPR-Cas9 responses.
  • Integration of support for diverse CRISPR guide RNA libraries and automated data processing.

Main Results:

  • CRISPRcleanR web application offers an intuitive interface, eliminating the need for R/python programming.
  • The platform provides a complete analytical pipeline with no pre-processing required.
  • Users receive gene-level essentiality summaries with statistical scores and interactive plots.
  • Enhanced support for a wider range of CRISPR guide RNA libraries compared to the original package.

Conclusions:

  • CRISPRcleanR web application democratizes the use of advanced CRISPR screen analysis.
  • The tool effectively reduces false positives, improving the reliability of essential gene identification.
  • This accessible platform facilitates more accurate and comprehensive genetic dependency studies.