CRISPR-FOCUS: A web server for designing focused CRISPR screening experiments.
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 (sgRN...
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2017-01-01
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| Series: | PLoS ONE |
| Online Access: | https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0184281&type=printable |
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| author | Qingyi Cao Jian Ma Chen-Hao Chen Han Xu Zhi Chen Wei Li X Shirley Liu |
| author_facet | Qingyi Cao Jian Ma Chen-Hao Chen Han Xu Zhi Chen Wei Li X Shirley Liu |
| author_sort | Qingyi Cao |
| collection | DOAJ |
| description | 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/). |
| format | Article |
| id | doaj-art-414e3441c69844fa9492a2d677a45e4a |
| institution | DOAJ |
| issn | 1932-6203 |
| language | English |
| publishDate | 2017-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj-art-414e3441c69844fa9492a2d677a45e4a2025-08-20T02:45:23ZengPublic Library of Science (PLoS)PLoS ONE1932-62032017-01-01129e018428110.1371/journal.pone.0184281CRISPR-FOCUS: A web server for designing focused CRISPR screening experiments.Qingyi CaoJian MaChen-Hao ChenHan XuZhi ChenWei LiX Shirley LiuThe 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/).https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0184281&type=printable |
| spellingShingle | Qingyi Cao Jian Ma Chen-Hao Chen Han Xu Zhi Chen Wei Li X Shirley Liu CRISPR-FOCUS: A web server for designing focused CRISPR screening experiments. PLoS ONE |
| title | CRISPR-FOCUS: A web server for designing focused CRISPR screening experiments. |
| title_full | CRISPR-FOCUS: A web server for designing focused CRISPR screening experiments. |
| title_fullStr | CRISPR-FOCUS: A web server for designing focused CRISPR screening experiments. |
| title_full_unstemmed | CRISPR-FOCUS: A web server for designing focused CRISPR screening experiments. |
| title_short | CRISPR-FOCUS: A web server for designing focused CRISPR screening experiments. |
| title_sort | crispr focus a web server for designing focused crispr screening experiments |
| url | https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0184281&type=printable |
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