Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

MAUDE: Inferring expression changes in sorting-based CRISPR screens

View ORCID ProfileCarl G. de Boer, John P. Ray, Nir Hacohen, View ORCID ProfileAviv Regev
doi: https://doi.org/10.1101/819649
Carl G. de Boer
1Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
2Klarman Cell Observatory, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Carl G. de Boer
  • For correspondence: carlgdeboer@gmail.com aregev@broadinstitute.org
John P. Ray
1Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Nir Hacohen
1Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
3Center for Cancer Research, Massachusetts General Hospital, Boston, MA 02114, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Aviv Regev
1Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
2Klarman Cell Observatory, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
4Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
5Howard Hughes Medical Institute, Cambridge, MA 02142
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Aviv Regev
  • For correspondence: carlgdeboer@gmail.com aregev@broadinstitute.org
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Data/Code
  • Preview PDF
Loading

Abstract

Pooled CRISPR screens allow high-throughput interrogation of genetic elements that alter expression of a reporter gene readout. New computational methods are needed to model these data. We created MAUDE (Mean Alterations Using Discrete Expression) for quantifying the impact of guide RNAs on a target gene’s expression in a pooled, sorting-based expression screen. MAUDE quantifies guide-level effects by modeling the distribution of cells across sorting expression bins. It then combines guides to estimate the statistical significance and effect size of targeted genetic elements. We show that MAUDE significantly improves over previous approaches and provide experimental design guidelines to best leverage MAUDE.

Footnotes

  • https://github.com/Carldeboer/MAUDE

  • Abbreviations

    AUROC
    Area under the receiver operating characteristic curve
    CaRE
    CRISPRa responsive element (as identified in 9)
    CRISPR
    clustered regularly interspaced short palindromic repeats
    FDR
    false discovery rate
    MAUDE
    mean alterations using discrete expression
    SD
    standard deviation
    TSS
    transcription start site
  • Copyright 
    The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
    Back to top
    PreviousNext
    Posted October 28, 2019.
    Download PDF
    Data/Code
    Email

    Thank you for your interest in spreading the word about bioRxiv.

    NOTE: Your email address is requested solely to identify you as the sender of this article.

    Enter multiple addresses on separate lines or separate them with commas.
    MAUDE: Inferring expression changes in sorting-based CRISPR screens
    (Your Name) has forwarded a page to you from bioRxiv
    (Your Name) thought you would like to see this page from the bioRxiv website.
    CAPTCHA
    This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
    Share
    MAUDE: Inferring expression changes in sorting-based CRISPR screens
    Carl G. de Boer, John P. Ray, Nir Hacohen, Aviv Regev
    bioRxiv 819649; doi: https://doi.org/10.1101/819649
    Digg logo Reddit logo Twitter logo Facebook logo Google logo LinkedIn logo Mendeley logo
    Citation Tools
    MAUDE: Inferring expression changes in sorting-based CRISPR screens
    Carl G. de Boer, John P. Ray, Nir Hacohen, Aviv Regev
    bioRxiv 819649; doi: https://doi.org/10.1101/819649

    Citation Manager Formats

    • BibTeX
    • Bookends
    • EasyBib
    • EndNote (tagged)
    • EndNote 8 (xml)
    • Medlars
    • Mendeley
    • Papers
    • RefWorks Tagged
    • Ref Manager
    • RIS
    • Zotero
    • Tweet Widget
    • Facebook Like
    • Google Plus One

    Subject Area

    • Bioinformatics
    Subject Areas
    All Articles
    • Animal Behavior and Cognition (3579)
    • Biochemistry (7523)
    • Bioengineering (5486)
    • Bioinformatics (20699)
    • Biophysics (10260)
    • Cancer Biology (7939)
    • Cell Biology (11584)
    • Clinical Trials (138)
    • Developmental Biology (6573)
    • Ecology (10144)
    • Epidemiology (2065)
    • Evolutionary Biology (13551)
    • Genetics (9502)
    • Genomics (12793)
    • Immunology (7887)
    • Microbiology (19456)
    • Molecular Biology (7618)
    • Neuroscience (41913)
    • Paleontology (307)
    • Pathology (1253)
    • Pharmacology and Toxicology (2181)
    • Physiology (3253)
    • Plant Biology (7008)
    • Scientific Communication and Education (1291)
    • Synthetic Biology (1942)
    • Systems Biology (5410)
    • Zoology (1108)