Literature DB >> 33478580

Minimal genome-wide human CRISPR-Cas9 library.

Emanuel Gonçalves1, Mark Thomas1, Fiona M Behan1, Gabriele Picco1, Clare Pacini1,2, Felicity Allen1, Alessandro Vinceti3, Mamta Sharma1, David A Jackson1, Stacey Price1, Charlotte M Beaver1, Oliver Dovey1, David Parry-Smith1, Francesco Iorio1,3, Leopold Parts1,4, Kosuke Yusa5, Mathew J Garnett6.   

Abstract

CRISPR guide RNA libraries have been iteratively improved to provide increasingly efficient reagents, although their large size is a barrier for many applications. We design an optimised minimal genome-wide human CRISPR-Cas9 library (MinLibCas9) by mining existing large-scale gene loss-of-function datasets, resulting in a greater than 42% reduction in size compared to other CRISPR-Cas9 libraries while preserving assay sensitivity and specificity. MinLibCas9 provides backward compatibility with existing datasets, increases the dynamic range of CRISPR-Cas9 screens and extends their application to complex models and assays.

Entities:  

Keywords:  CRISPR-Cas9; Genome-wide; KS score; Minimal library; Organoid

Mesh：

Substances：

Year:  2021        PMID： 33478580      PMCID： PMC7818936          DOI： 10.1186/s13059-021-02268-4

Source DB:  PubMed          Journal:  Genome Biol        ISSN： 1474-7596            Impact factor:   13.583


  46 in total

1.  High-Resolution CRISPR Screens Reveal Fitness Genes and Genotype-Specific Cancer Liabilities.

Authors:  Traver Hart; Megha Chandrashekhar; Michael Aregger; Zachary Steinhart; Kevin R Brown; Graham MacLeod; Monika Mis; Michal Zimmermann; Amelie Fradet-Turcotte; Song Sun; Patricia Mero; Peter Dirks; Sachdev Sidhu; Frederick P Roth; Olivia S Rissland; Daniel Durocher; Stephane Angers; Jason Moffat
Journal:  Cell       Date:  2015-11-25       Impact factor: 41.582

2.  A genome-wide CRISPR screen identifies a restricted set of HIV host dependency factors.

Authors:  Ryan J Park; Tim Wang; Dylan Koundakjian; Judd F Hultquist; Pedro Lamothe-Molina; Blandine Monel; Kathrin Schumann; Haiyan Yu; Kevin M Krupzcak; Wilfredo Garcia-Beltran; Alicja Piechocka-Trocha; Nevan J Krogan; Alexander Marson; David M Sabatini; Eric S Lander; Nir Hacohen; Bruce D Walker
Journal:  Nat Genet       Date:  2016-12-19       Impact factor: 38.330

3.  A CRISPR-Based Screen Identifies Genes Essential for West-Nile-Virus-Induced Cell Death.

Authors:  Hongming Ma; Ying Dang; Yonggan Wu; Gengxiang Jia; Edgar Anaya; Junli Zhang; Sojan Abraham; Jang-Gi Choi; Guojun Shi; Ling Qi; N Manjunath; Haoquan Wu
Journal:  Cell Rep       Date:  2015-07-16       Impact factor: 9.423

4.  Prioritization of cancer therapeutic targets using CRISPR-Cas9 screens.

Authors:  Fiona M Behan; Francesco Iorio; Gabriele Picco; Kosuke Yusa; Mathew J Garnett; Emanuel Gonçalves; Charlotte M Beaver; Giorgia Migliardi; Rita Santos; Yanhua Rao; Francesco Sassi; Marika Pinnelli; Rizwan Ansari; Sarah Harper; David Adam Jackson; Rebecca McRae; Rachel Pooley; Piers Wilkinson; Dieudonne van der Meer; David Dow; Carolyn Buser-Doepner; Andrea Bertotti; Livio Trusolino; Euan A Stronach; Julio Saez-Rodriguez
Journal:  Nature       Date:  2019-04-10       Impact factor: 49.962

5.  A Multiplexed Single-Cell CRISPR Screening Platform Enables Systematic Dissection of the Unfolded Protein Response.

Authors:  Britt Adamson; Thomas M Norman; Marco Jost; Min Y Cho; James K Nuñez; Yuwen Chen; Jacqueline E Villalta; Luke A Gilbert; Max A Horlbeck; Marco Y Hein; Ryan A Pak; Andrew N Gray; Carol A Gross; Atray Dixit; Oren Parnas; Aviv Regev; Jonathan S Weissman
Journal:  Cell       Date:  2016-12-15       Impact factor: 41.582

6.  Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens.

Authors:  Atray Dixit; Oren Parnas; Biyu Li; Jenny Chen; Charles P Fulco; Livnat Jerby-Arnon; Nemanja D Marjanovic; Danielle Dionne; Tyler Burks; Raktima Raychowdhury; Britt Adamson; Thomas M Norman; Eric S Lander; Jonathan S Weissman; Nir Friedman; Aviv Regev
Journal:  Cell       Date:  2016-12-15       Impact factor: 41.582

7.  Discovery of cancer drug targets by CRISPR-Cas9 screening of protein domains.

Authors:  Junwei Shi; Eric Wang; Joseph P Milazzo; Zihua Wang; Justin B Kinney; Christopher R Vakoc
Journal:  Nat Biotechnol       Date:  2015-05-11       Impact factor: 54.908

8.  BAGEL: a computational framework for identifying essential genes from pooled library screens.

Authors:  Traver Hart; Jason Moffat
Journal:  BMC Bioinformatics       Date:  2016-04-16       Impact factor: 3.169

9.  Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR.

Authors:  Maximilian Haeussler; Kai Schönig; Hélène Eckert; Alexis Eschstruth; Joffrey Mianné; Jean-Baptiste Renaud; Sylvie Schneider-Maunoury; Alena Shkumatava; Lydia Teboul; Jim Kent; Jean-Stephane Joly; Jean-Paul Concordet
Journal:  Genome Biol       Date:  2016-07-05       Impact factor: 13.583

10.  The Pfam protein families database in 2019.

Authors:  Sara El-Gebali; Jaina Mistry; Alex Bateman; Sean R Eddy; Aurélien Luciani; Simon C Potter; Matloob Qureshi; Lorna J Richardson; Gustavo A Salazar; Alfredo Smart; Erik L L Sonnhammer; Layla Hirsh; Lisanna Paladin; Damiano Piovesan; Silvio C E Tosatto; Robert D Finn
Journal:  Nucleic Acids Res       Date:  2019-01-08       Impact factor: 16.971
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  9 in total

Review 1.  A new era in functional genomics screens.

Authors:  Laralynne Przybyla; Luke A Gilbert
Journal:  Nat Rev Genet       Date:  2021-09-20       Impact factor: 53.242

Review 2.  Computational estimation of quality and clinical relevance of cancer cell lines.

Authors:  Lucia Trastulla; Javad Noorbakhsh; Francisca Vazquez; James McFarland; Francesco Iorio
Journal:  Mol Syst Biol       Date:  2022-07       Impact factor: 13.068

Review 3.  CRISPR/Cas9: Principle, Applications, and Delivery through Extracellular Vesicles.

Authors:  Katarzyna Horodecka; Markus Düchler
Journal:  Int J Mol Sci       Date:  2021-06-04       Impact factor: 5.923

4.  Integrated cross-study datasets of genetic dependencies in cancer.

Authors:  Clare Pacini; Joshua M Dempster; Isabella Boyle; Emanuel Gonçalves; Hanna Najgebauer; Emre Karakoc; Dieudonne van der Meer; Andrew Barthorpe; Howard Lightfoot; Patricia Jaaks; James M McFarland; Mathew J Garnett; Aviad Tsherniak; Francesco Iorio
Journal:  Nat Commun       Date:  2021-03-12       Impact factor: 14.919

Review 5.  Common computational tools for analyzing CRISPR screens.

Authors:  Medina Colic; Traver Hart
Journal:  Emerg Top Life Sci       Date:  2021-12-21

Review 6.  Strategies for genetic manipulation of adult stem cell-derived organoids.

Authors:  Constantin Menche; Henner F Farin
Journal:  Exp Mol Med       Date:  2021-10-18       Impact factor: 8.718

Review 7.  To Discover the Efficient and Novel Drug Targets in Human Cancers Using CRISPR/Cas Screening and Databases.

Authors:  Iichiroh Onishi; Kouhei Yamamoto; Yuko Kinowaki; Masanobu Kitagawa; Morito Kurata
Journal:  Int J Mol Sci       Date:  2021-11-15       Impact factor: 5.923

8.  A suspension technique for efficient large-scale cancer organoid culturing and perturbation screens.

Authors:  Stacey Price; Shriram Bhosle; Emanuel Gonçalves; Xiaodun Li; Dylan P McClurg; Syd Barthorpe; Alex Beck; Caitlin Hall; Howard Lightfoot; Luke Farrow; Rizwan Ansari; David A Jackson; Laura Allen; Kirsty Roberts; Charlotte Beaver; Hayley E Francies; Mathew J Garnett
Journal:  Sci Rep       Date:  2022-04-02       Impact factor: 4.379

9.  Comparative optimization of combinatorial CRISPR screens.

Authors:  Davide Monducci; Michael J Young; Ruitong Li; Olaf Klingbeil; Diego J Rodriguez; Zaid Bayyat; Joshua M Dempster; Devishi Kesar; Xiaoping Yang; Mahdi Zamanighomi; Christopher R Vakoc; Takahiro Ito; William R Sellers
Journal:  Nat Commun       Date:  2022-05-05       Impact factor: 17.694
  9 in total

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