Green listed—a CRISPR screen tool

Panda, Santanu; Boddul, Sanjay V.; Jiménez-Andrade, Guillermina Yanek; Jiang, Long; Kasza, Zsolt; Fernandez-Ricaud, Luciano; Wermeling, Fredrik

doi:10.1093/bioinformatics/btw739

Cited by 11 publications

(13 citation statements)

References 12 publications

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“…gRNAs with matching overhangs for the respective plasmids were extracted from the Green Listed software (http://greenlisted. cmm.ki.se/), described in Panda et al (69), using the Brie reference library (70). gRNA oligomers for pSpCas9(BB)-2A-Puro (PX459) V2.0 (Addgene plasmid #62988; kindly provided by Feng Zhang, Broad Institute of MIT and Harvard, Cambridge, MA) experiments were ordered as sense and antisense 80-mers (SI Appendix, Table S2) and as sense 70-or 100-mers for the lentiGuide-Puro-P2A-EGFP_mRFPstuf experiments (SI Appendix, Tables S3 and S4).…”

Section: Methodsmentioning

confidence: 99%

IL-4 controls activated neutrophil FcγR2b expression and migration into inflamed joints

Panda

Wigerblad

Jiang

et al. 2020

Proc. Natl. Acad. Sci. U.S.A.

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Neutrophils are the most abundant immune cells found in actively inflamed joints of patients with rheumatoid arthritis (RA), and most animal models for RA depend on neutrophils for the induction of joint inflammation. Exogenous IL-4 and IL-13 protect mice from antibody-mediated joint inflammation, although the mechanism is not understood. Neutrophils display a very strong basal expression of STAT6, which is responsible for signaling following exposure to IL-4 and IL-13. Still, the role of IL-4 and IL-13 in neutrophil biology has not been well studied. This can be explained by the low neutrophil surface expression of the IL-4 receptor α-chain (IL-4Rα), essential for IL-4– and IL-13–induced STAT6 signaling. Here we identify that colony stimulating factor 3 (CSF3), released during acute inflammation, mediates potent STAT3-dependent neutrophil IL-4Rα up-regulation during sterile inflammatory conditions. We further demonstrate that IL-4 limits neutrophil migration to inflamed joints, and that CSF3 combined with IL-4 or IL-13 results in a prominent neutrophil up-regulation of the inhibitory Fcγ receptor (FcγR2b). Taking these data together, we demonstrate that the IL-4 and CSF3 pathways are linked and play important roles in regulating proinflammatory neutrophil behavior.

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Section: Methodsmentioning

confidence: 99%

IL-4 controls activated neutrophil FcγR2b expression and migration into inflamed joints

Panda

Wigerblad

Jiang

et al. 2020

Proc. Natl. Acad. Sci. U.S.A.

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“…In practice, NTC sets are commonly slightly enriched, due to the absence of DNA damage induced by the NTC in contrast to targeting gRNAs. A resource to extract lists of negative control gRNAs for mouse and human can be found using the ‘Green Listed’ tool [84] . Pressing “detailed information” in the Zhang/GeCKOv2 or Wang/Lander/Sabatini reference libraries provides more information.…”

Section: How To Design a Hypothesis-driven Custom Screenmentioning

confidence: 99%

“…After generating a list of genes and controls to include in a custom screen, we typically use the free web-based ‘Green Listed’ tool for rapid gRNA design, something we have successfully used for several published and unpublished custom screens [84] , [86] . Extensive information about how to work with the tool can be found on the webpage, as well as in [1] .…”

Section: How To Design a Hypothesis-driven Custom Screenmentioning

confidence: 99%

Designing custom CRISPR libraries for hypothesis-driven drug target discovery

Iyer

Jiang

Shen

et al. 2020

Computational and Structural Biotechnology Journal

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Over the last decade Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) has been developed into a potent molecular biology tool used to rapidly modify genes or their expression in a multitude of ways. In parallel, CRISPR-based screening approaches have been developed as powerful discovery platforms for dissecting the genetic basis of cellular behavior, as well as for drug target discovery. CRISPR screens can be designed in numerous ways. Here, we give a brief background to CRISPR screens and discuss the pros and cons of different design approaches, including unbiased genome-wide screens that target all known genes, as well as hypothesis-driven custom screens in which selected subsets of genes are targeted ( Fig. 1 ). We provide several suggestions for how a custom screen can be designed, which could broadly serve as inspiration for any experiment that includes candidate gene selection. Finally, we discuss how results from CRISPR screens could be translated into drug development, as well as future trends we foresee in the rapidly evolving CRISPR screen field.

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“…To design libraries for CRISPR screens (especially focused screens), several computational tools can be applied [ 19 , 21 – 30 ]. However, most of these algorithms provide optimized sgRNAs for only one or several genes/sequences [ 22 – 23 , 29 ].…”

Section: Introductionmentioning

confidence: 99%

“…However, most of these algorithms provide optimized sgRNAs for only one or several genes/sequences [ 22 – 23 , 29 ]. A few web-based tools with nominal batch design capacity require users to provide target sequence for each individual gene, have strict size limits on the sequence file uploaded, could only accept limited numbers (10–20 mostly) of gene IDs as input, or base their work on mining of public domain libraries [ 19 , 25 – 26 , 30 ]. Some other tools with substantial batch-design capacity are not web-based, and require users to download the whole database, compile the source code and fine tune up to dozens of parameters [ 21 , 24 , 27 – 28 ].…”

Section: Introductionmentioning

confidence: 99%

CRISPR-FOCUS: A web server for designing focused CRISPR screening experiments

Cao

Chen

et al. 2017

PLoS ONE

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The recently developed CRISPR screen technology, based on the CRISPR/Cas9 genome editing system, enables genome-wide interrogation of gene functions in an efficient and cost-effective manner. Although many computational algorithms and web servers have been developed to design single-guide RNAs (sgRNAs) with high specificity and efficiency, algorithms specifically designed for conducting CRISPR screens are still lacking. Here we present CRISPR-FOCUS, a web-based platform to search and prioritize sgRNAs for CRISPR screen experiments. With official gene symbols or RefSeq IDs as the only mandatory input, CRISPR-FOCUS filters and prioritizes sgRNAs based on multiple criteria, including efficiency, specificity, sequence conservation, isoform structure, as well as genomic variations including Single Nucleotide Polymorphisms and cancer somatic mutations. CRISPR-FOCUS also provides pre-defined positive and negative control sgRNAs, as well as other necessary sequences in the construct (e.g., U6 promoters to drive sgRNA transcription and RNA scaffolds of the CRISPR/Cas9). These features allow users to synthesize oligonucleotides directly based on the output of CRISPR-FOCUS. Overall, CRISPR-FOCUS provides a rational and high-throughput approach for sgRNA library design that enables users to efficiently conduct a focused screen experiment targeting up to thousands of genes.(CRISPR-FOCUS is freely available at http://cistrome.org/crispr-focus/)

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Green listed—a CRISPR screen tool

Abstract: fredrik.wermeling@ki.se.

Cited by 11 publications

References 12 publications

IL-4 controls activated neutrophil FcγR2b expression and migration into inflamed joints

IL-4 controls activated neutrophil FcγR2b expression and migration into inflamed joints

Designing custom CRISPR libraries for hypothesis-driven drug target discovery

CRISPR-FOCUS: A web server for designing focused CRISPR screening experiments

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