publication . Article . 2014

edgeR: a versatile tool for the analysis of shRNA-seq and CRISPR-Cas9 genetic screens.

Zhiyin Dai; Julie M. Sheridan; Linden J. Gearing; Darcy L. Moore; Shian Su; Sam Wormald; Stephen Wilcox; Liam O'Connor; Ross A. Dickins; Marnie E. Blewitt; ...
Open Access English
  • Published: 01 Oct 2014 Journal: F1000Research, volume 3 (eissn: 2046-1402, Copyright policy)
  • Publisher: F1000Research
Abstract
<ns4:p>Pooled library sequencing screens that perturb gene function in a high-throughput manner are becoming increasingly popular in functional genomics research. Irrespective of the mechanism by which loss of function is achieved, via either RNA interference using short hairpin RNAs (shRNAs) or genetic mutation using single guide RNAs (sgRNAs) with the CRISPR-Cas9 system, there is a need to establish optimal analysis tools to handle such data. Our open-source processing pipeline in edgeR provides a complete analysis solution for screen data, that begins with the raw sequence reads and ends with a ranked list of candidate genes for downstream biological validati...
Subjects
free text keywords: Software Tool Article, Articles, Bioinformatics, Medicine, R, Science, Q, Biology, FASTQ format, Workflow, Genetic screen, CRISPR, Neuroscience, Ranking, Computational biology, Functional genomics, Normalization (statistics), Row
Funded by
NHMRC| Identification of novel epigenetic modifiers involved in neural stem cell function and glioblastoma
Project
  • Funder: National Health and Medical Research Council (NHMRC) (NHMRC)
  • Project Code: 1059622
  • Funding stream: Project Grants
,
NHMRC| Statistical methods for next-generation genomics
Project
  • Funder: National Health and Medical Research Council (NHMRC) (NHMRC)
  • Project Code: 1050661
  • Funding stream: Project Grants
23 references, page 1 of 2

1 Bassik MC Lebbink RJ Churchman LS: Rapid creation and quantitative monitoring of high coverage shRNA libraries.Nat Methods.2009;6(6):443–5. 10.1038/nmeth.1330 19448642 [OpenAIRE] [PubMed] [DOI]

2 Wang T Wei JJ Sabatini DM: Genetic screens in human cells using the CRISPR/Cas9 system.Science.2014;343(6166):80–4. 10.1126/science.1246981 24336569 [OpenAIRE] [PubMed] [DOI]

3 Zuber J Shi J Wang E: RNAi screen identifies Brd4 as a therapeutic target in acute myeloid leukaemia.Nature.2011;478(7370):524–8. 10.1038/nature10334 21814200 [OpenAIRE] [PubMed] [DOI]

4 Sullivan KD Padilla-Just N Henry RE: ATM and MET kinases are synthetic lethal with nongenotoxic activation of p53.Nat Chem Biol.2012;8(7):646–54. 10.1038/nchembio.965 22660439 [OpenAIRE] [PubMed] [DOI]

5 Bassik MC Kampmann M Lebbink RJ: A systematic mammalian genetic interaction map reveals pathways underlying ricin susceptibility.Cell.2013;152(4):909–22. 10.1016/j.cell.2013.01.030 23394947 [OpenAIRE] [PubMed] [DOI]

6 Shalem O Sanjana NE Hartenian E: Genome-scale CRISPR-Cas9 knockout screening in human cells.Science.2014;343(6166):84–7. 10.1126/science.1247005 24336571 [OpenAIRE] [PubMed] [DOI]

7 Tijsterman M Plasterk RH: Dicers at RISC; the mechanism of RNai.Cell.2004;117(1):1–3. 10.1016/S0092-8674(04)00293-4 15066275 [OpenAIRE] [PubMed] [DOI]

8 Mali P Esvelt KM Church GM: Cas9 as a versatile tool for engineering biology.Nat Methods.2013;10(10):957–63. 10.1038/nmeth.2649 24076990 [OpenAIRE] [PubMed] [DOI]

9 Sims D Mendes-Pereira AM Frankum J: High-throughput RNA interference screening using pooled shRNA libraries and next generation sequencing.Genome Biol.2011;12(10):R104. 10.1186/gb-2011-12-10-r104 22018332 [OpenAIRE] [PubMed] [DOI]

10 Kim J Tan AC: BiNGS!SL-seq: a bioinformatics pipeline for the analysis and interpretation of deep sequencing genome-wide synthetic lethal screen.Methods Mol Biol.2012;802:389–98. 10.1007/978-1-61779-400-1_26 22130895 [OpenAIRE] [PubMed] [DOI]

11 Robinson MD McCarthy DJ Smyth GK: edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.Bioinformatics.2010;26(1):139–40. 10.1093/bioinformatics/btp616 19910308 [OpenAIRE] [PubMed] [DOI]

12 Gentleman RC Carey VJ Bates DM: Bioconductor: open software development for computational biology and bioinformatics.Genome Biol.2004;5(10):R80. 10.1186/gb-2004-5-10-r80 15461798 [OpenAIRE] [PubMed] [DOI]

13 R Core Team. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria,2014 Reference Source

14 Robinson MD Smyth GK: Small-sample estimation of negative binomial dispersion, with applications to sage data.Biostatistics.2008;9(2):321–32. 10.1093/biostatistics/kxm030 17728317 [OpenAIRE] [PubMed] [DOI]

15 McCarthy DJ Chen Y Smyth GK: Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation.Nucleic Acids Res.2012;40(10):4288–97. 10.1093/nar/gks042 22287627 [OpenAIRE] [PubMed] [DOI]

23 references, page 1 of 2
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