A comprehensive protocol resource for performing pooled shRNA and CRISPR screens

Leonie A. Cluse, Iva Nikolic, Deborah Knight, Piyush B. Madhamshettiwar, Jennii Luu, Karla J. Cowley, Timothy Semple, Gisela Mir Arnau, Jake Shortt, Ricky W. Johnstone, Kaylene J. Simpson

Research output: Chapter in Book/Report/Conference proceedingChapter (Book)Otherpeer-review

1 Citation (Scopus)

Abstract

This chapter details a compendium of protocols that collectively enable the reader to perform a pooled shRNA and/or CRISPR screen—with methods to identify and validate positive controls and subsequent hits; establish a viral titer in the cell line of choice; create and screen libraries, sequence strategies, and bioinformatics resources to analyze outcomes. Collectively, this provides an overarching resource from the start to finish of a screening project, making this technology possible in all laboratories.

Original languageEnglish
Title of host publicationMethods in Molecular Biology
EditorsJohn M. Walker
Place of PublicationNew York, NY
PublisherHumana Press
Chapter17
Pages201-227
Number of pages27
ISBN (Electronic)9781493975686
ISBN (Print)9781493975679
DOIs
Publication statusPublished - 2018

Publication series

NameMethods in Molecular Biology
PublisherHumana Press, Inc.
Volume1725
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029

Keywords

  • Drop out screen
  • Lentivirus
  • Pooled CRISPR
  • Pooled shRNA

Cite this

Cluse, L. A., Nikolic, I., Knight, D., Madhamshettiwar, P. B., Luu, J., Cowley, K. J., ... Simpson, K. J. (2018). A comprehensive protocol resource for performing pooled shRNA and CRISPR screens. In J. M. Walker (Ed.), Methods in Molecular Biology (pp. 201-227). (Methods in Molecular Biology; Vol. 1725). New York, NY: Humana Press. https://doi.org/10.1007/978-1-4939-7568-6_17
Cluse, Leonie A. ; Nikolic, Iva ; Knight, Deborah ; Madhamshettiwar, Piyush B. ; Luu, Jennii ; Cowley, Karla J. ; Semple, Timothy ; Arnau, Gisela Mir ; Shortt, Jake ; Johnstone, Ricky W. ; Simpson, Kaylene J. / A comprehensive protocol resource for performing pooled shRNA and CRISPR screens. Methods in Molecular Biology. editor / John M. Walker. New York, NY : Humana Press, 2018. pp. 201-227 (Methods in Molecular Biology).
@inbook{2d9291381b73472a9a8be38ee3f9dabc,
title = "A comprehensive protocol resource for performing pooled shRNA and CRISPR screens",
abstract = "This chapter details a compendium of protocols that collectively enable the reader to perform a pooled shRNA and/or CRISPR screen—with methods to identify and validate positive controls and subsequent hits; establish a viral titer in the cell line of choice; create and screen libraries, sequence strategies, and bioinformatics resources to analyze outcomes. Collectively, this provides an overarching resource from the start to finish of a screening project, making this technology possible in all laboratories.",
keywords = "Drop out screen, Lentivirus, Pooled CRISPR, Pooled shRNA",
author = "Cluse, {Leonie A.} and Iva Nikolic and Deborah Knight and Madhamshettiwar, {Piyush B.} and Jennii Luu and Cowley, {Karla J.} and Timothy Semple and Arnau, {Gisela Mir} and Jake Shortt and Johnstone, {Ricky W.} and Simpson, {Kaylene J.}",
year = "2018",
doi = "10.1007/978-1-4939-7568-6_17",
language = "English",
isbn = "9781493975679",
series = "Methods in Molecular Biology",
publisher = "Humana Press",
pages = "201--227",
editor = "Walker, {John M. }",
booktitle = "Methods in Molecular Biology",
address = "United States of America",

}

Cluse, LA, Nikolic, I, Knight, D, Madhamshettiwar, PB, Luu, J, Cowley, KJ, Semple, T, Arnau, GM, Shortt, J, Johnstone, RW & Simpson, KJ 2018, A comprehensive protocol resource for performing pooled shRNA and CRISPR screens. in JM Walker (ed.), Methods in Molecular Biology. Methods in Molecular Biology, vol. 1725, Humana Press, New York, NY, pp. 201-227. https://doi.org/10.1007/978-1-4939-7568-6_17

A comprehensive protocol resource for performing pooled shRNA and CRISPR screens. / Cluse, Leonie A.; Nikolic, Iva; Knight, Deborah; Madhamshettiwar, Piyush B.; Luu, Jennii; Cowley, Karla J.; Semple, Timothy; Arnau, Gisela Mir; Shortt, Jake; Johnstone, Ricky W.; Simpson, Kaylene J.

Methods in Molecular Biology. ed. / John M. Walker. New York, NY : Humana Press, 2018. p. 201-227 (Methods in Molecular Biology; Vol. 1725).

Research output: Chapter in Book/Report/Conference proceedingChapter (Book)Otherpeer-review

TY - CHAP

T1 - A comprehensive protocol resource for performing pooled shRNA and CRISPR screens

AU - Cluse, Leonie A.

AU - Nikolic, Iva

AU - Knight, Deborah

AU - Madhamshettiwar, Piyush B.

AU - Luu, Jennii

AU - Cowley, Karla J.

AU - Semple, Timothy

AU - Arnau, Gisela Mir

AU - Shortt, Jake

AU - Johnstone, Ricky W.

AU - Simpson, Kaylene J.

PY - 2018

Y1 - 2018

N2 - This chapter details a compendium of protocols that collectively enable the reader to perform a pooled shRNA and/or CRISPR screen—with methods to identify and validate positive controls and subsequent hits; establish a viral titer in the cell line of choice; create and screen libraries, sequence strategies, and bioinformatics resources to analyze outcomes. Collectively, this provides an overarching resource from the start to finish of a screening project, making this technology possible in all laboratories.

AB - This chapter details a compendium of protocols that collectively enable the reader to perform a pooled shRNA and/or CRISPR screen—with methods to identify and validate positive controls and subsequent hits; establish a viral titer in the cell line of choice; create and screen libraries, sequence strategies, and bioinformatics resources to analyze outcomes. Collectively, this provides an overarching resource from the start to finish of a screening project, making this technology possible in all laboratories.

KW - Drop out screen

KW - Lentivirus

KW - Pooled CRISPR

KW - Pooled shRNA

UR - http://www.scopus.com/inward/record.url?scp=85040695335&partnerID=8YFLogxK

U2 - 10.1007/978-1-4939-7568-6_17

DO - 10.1007/978-1-4939-7568-6_17

M3 - Chapter (Book)

SN - 9781493975679

T3 - Methods in Molecular Biology

SP - 201

EP - 227

BT - Methods in Molecular Biology

A2 - Walker, John M.

PB - Humana Press

CY - New York, NY

ER -

Cluse LA, Nikolic I, Knight D, Madhamshettiwar PB, Luu J, Cowley KJ et al. A comprehensive protocol resource for performing pooled shRNA and CRISPR screens. In Walker JM, editor, Methods in Molecular Biology. New York, NY: Humana Press. 2018. p. 201-227. (Methods in Molecular Biology). https://doi.org/10.1007/978-1-4939-7568-6_17