MAGeCKFlute is distinguished from other currently available tools by its comprehensive pipeline, which contains a series of functions for analyzing CRISPR screen data. This protocol explains how to use MAGeCKFlute to perform quality control (QC), normalization, batch effect removal, copy-number bias ...
然而,单纯的设计一条或多条sgRNA(single guide RNA)进行基因敲低,这样的实验方法通量过低,因此,借鉴shRNA Screen技术,许多团队开发出版本各异的Cas9 Screen技术。 我查询到的最早版本的Cas9 screen来自两篇背靠背Science paper,分别出自Broad研究所张锋团队和Langer与Sabitini团队[1][2]。在张锋团队发表的这篇文章中,...
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protocol for genome-scale knockout and transcriptional activation screening using the CRISPR-Cas9 system. Custom- or ready-made guide RNA libraries are constructed and packaged into lentiviral vectors for delivery into cells for screening. As each screen is unique, we provide guidelines for determining...
Nature Microbiology(2024) A genome-wide CRISPR/Cas9 knockout screen identifies SEMA3F gene for resistance to cyclin-dependent kinase 4 and 6 inhibitors in breast cancer Yuko Kawai Aiko Nagayama Yuko Kitagawa Breast Cancer(2024) Sections Figures ...
PCa genetic risk SNPs are enriched in noncoding CREs rather than in protein-coding regions9,80. It is challenging to systematically evaluate the importance of these rCREs in cancer biology and the clinic. Our study demonstrates that CRISPRi mediated loss-of-function screen of rCREs is an effic...
Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. Extended data figures and tables Extended Data Fig. 1 Mevalonate pathway effects, co-culture screen consistency, and gene set enrichment analysis (GSEA). (a) Schematic...
For those who want to screen such cell lines, and particularly neurospheres, we provide a step-by-step description of assay development tests to be performed before screening, as well as for the screen itself. We highlight considerations of variables that make these screens distinct from, or ...
and A.K. performed the arrayed validation screen; A.F.R. and J.K. developed software; P.D., A.F.R., C.S., and T.K. analyzed data; P.D. and A.F.R. visualized data; P.D., A.F.R., C.S., and C.B. wrote the original draft; T.K., P.T., L.C.S., A.K., ...
About 15 million reads were obtained for each indexed screen. For some of the screens, an alternative strategy was used to accommodate sequencing on an Illumina NextSeq 500 platform. Changes to the protocol above include amplification of extracted gDNA by PCR using a barcoded forward primer (CC_...