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Optimized PCR Conditions and Increased shRNA Fold Representation Improve Reproducibility of Pooled shRNA Screens
RNAi screening using pooled shRNA libraries is a valuable tool for identifying genetic regulators of biological processes. However, for a successful pooled shRNA screen, it is imperative to thoroughly optimize experimental conditions to obtain reproducible data. Here we performed viability screens w...
Autores principales: | , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2012
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3411659/ https://www.ncbi.nlm.nih.gov/pubmed/22870320 http://dx.doi.org/10.1371/journal.pone.0042341 |
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author | Strezoska, Žaklina Licon, Abel Haimes, Josh Spayd, Katie Jansen Patel, Kruti M. Sullivan, Kevin Jastrzebski, Katarzyna Simpson, Kaylene J. Leake, Devin van Brabant Smith, Anja Vermeulen, Annaleen |
author_facet | Strezoska, Žaklina Licon, Abel Haimes, Josh Spayd, Katie Jansen Patel, Kruti M. Sullivan, Kevin Jastrzebski, Katarzyna Simpson, Kaylene J. Leake, Devin van Brabant Smith, Anja Vermeulen, Annaleen |
author_sort | Strezoska, Žaklina |
collection | PubMed |
description | RNAi screening using pooled shRNA libraries is a valuable tool for identifying genetic regulators of biological processes. However, for a successful pooled shRNA screen, it is imperative to thoroughly optimize experimental conditions to obtain reproducible data. Here we performed viability screens with a library of ∼10 000 shRNAs at two different fold representations (100- and 500-fold at transduction) and report the reproducibility of shRNA abundance changes between screening replicates determined by microarray and next generation sequencing analyses. We show that the technical reproducibility between PCR replicates from a pooled screen can be drastically improved by ensuring that PCR amplification steps are kept within the exponential phase and by using an amount of genomic DNA input in the reaction that maintains the average template copies per shRNA used during library transduction. Using these optimized PCR conditions, we then show that higher reproducibility of biological replicates is obtained by both microarray and next generation sequencing when screening with higher average shRNA fold representation. shRNAs that change abundance reproducibly in biological replicates (primary hits) are identified from screens performed with both 100- and 500-fold shRNA representation, however a higher percentage of primary hit overlap between screening replicates is obtained from 500-fold shRNA representation screens. While strong hits with larger changes in relative abundance were generally identified in both screens, hits with smaller changes were identified only in the screens performed with the higher shRNA fold representation at transduction. |
format | Online Article Text |
id | pubmed-3411659 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2012 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-34116592012-08-06 Optimized PCR Conditions and Increased shRNA Fold Representation Improve Reproducibility of Pooled shRNA Screens Strezoska, Žaklina Licon, Abel Haimes, Josh Spayd, Katie Jansen Patel, Kruti M. Sullivan, Kevin Jastrzebski, Katarzyna Simpson, Kaylene J. Leake, Devin van Brabant Smith, Anja Vermeulen, Annaleen PLoS One Research Article RNAi screening using pooled shRNA libraries is a valuable tool for identifying genetic regulators of biological processes. However, for a successful pooled shRNA screen, it is imperative to thoroughly optimize experimental conditions to obtain reproducible data. Here we performed viability screens with a library of ∼10 000 shRNAs at two different fold representations (100- and 500-fold at transduction) and report the reproducibility of shRNA abundance changes between screening replicates determined by microarray and next generation sequencing analyses. We show that the technical reproducibility between PCR replicates from a pooled screen can be drastically improved by ensuring that PCR amplification steps are kept within the exponential phase and by using an amount of genomic DNA input in the reaction that maintains the average template copies per shRNA used during library transduction. Using these optimized PCR conditions, we then show that higher reproducibility of biological replicates is obtained by both microarray and next generation sequencing when screening with higher average shRNA fold representation. shRNAs that change abundance reproducibly in biological replicates (primary hits) are identified from screens performed with both 100- and 500-fold shRNA representation, however a higher percentage of primary hit overlap between screening replicates is obtained from 500-fold shRNA representation screens. While strong hits with larger changes in relative abundance were generally identified in both screens, hits with smaller changes were identified only in the screens performed with the higher shRNA fold representation at transduction. Public Library of Science 2012-08-01 /pmc/articles/PMC3411659/ /pubmed/22870320 http://dx.doi.org/10.1371/journal.pone.0042341 Text en © 2012 Strezoska et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited. |
spellingShingle | Research Article Strezoska, Žaklina Licon, Abel Haimes, Josh Spayd, Katie Jansen Patel, Kruti M. Sullivan, Kevin Jastrzebski, Katarzyna Simpson, Kaylene J. Leake, Devin van Brabant Smith, Anja Vermeulen, Annaleen Optimized PCR Conditions and Increased shRNA Fold Representation Improve Reproducibility of Pooled shRNA Screens |
title | Optimized PCR Conditions and Increased shRNA Fold Representation Improve Reproducibility of Pooled shRNA Screens |
title_full | Optimized PCR Conditions and Increased shRNA Fold Representation Improve Reproducibility of Pooled shRNA Screens |
title_fullStr | Optimized PCR Conditions and Increased shRNA Fold Representation Improve Reproducibility of Pooled shRNA Screens |
title_full_unstemmed | Optimized PCR Conditions and Increased shRNA Fold Representation Improve Reproducibility of Pooled shRNA Screens |
title_short | Optimized PCR Conditions and Increased shRNA Fold Representation Improve Reproducibility of Pooled shRNA Screens |
title_sort | optimized pcr conditions and increased shrna fold representation improve reproducibility of pooled shrna screens |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3411659/ https://www.ncbi.nlm.nih.gov/pubmed/22870320 http://dx.doi.org/10.1371/journal.pone.0042341 |
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