CRISPR Dropout Screens Identify DHODH,PIK3C3, and Crkl as Potential Therapeutic Targets in Acute Myeloid LeukemiaRelapsed disease is still a major challenge in AML despite recently approved targeted therapies. New therapeutic targets are needed. To identify vulnerabilities in AML, screening data from a...
Also known as dropout screens. Cells with the phenotype of interest are depleted in the screen; other cells are maintained. Effective dose The intensity of a perturbation (such as a drug or virus) that causes an effect (such as cell death) in a specified percentage of cells. Screening hits...
BMC Genomics (2016) 17:723 DOI 10.1186/s12864-016-3042-2 METHODOLOGY ARTICLE Open Access Identification of oncogenic driver mutations by genome-wide CRISPR-Cas9 dropout screening Michael K. Kiessling1, Sven Schuierer2, Silke Stertz3, Martin Beibel2, Sebastian Bergling2, Judith Knehr2, Walter...
Despite the growing interest of archiving information in synthetic DNA to confront data explosion, quantitatively querying the data stored in DNA is still a challenge. Herein, we present Search Enabled by Enzymatic Keyword Recognition (SEEKER), which uti
1c). We investigated if low amino acid conditions altered transporter gene expression; low-Arg and low-Leu screening conditions increased expression of most genes in our SLC7 transporter panel, but not all of them, consistent with results for HEK293T cells in single amino acid dropout media35...
Recent genome-wide screening has revealed that essential genes account for ~ 10% of total human genes [6]. To study essential genes in cells, conditional knockout strategies have been developed. The Cre/loxP recombination system is the most commonly used technique to knockout essential genes....
Pooled CRISPR screening data in cancer cell lines is limited to Log2(fold changes) for PMAIP1 sgRNAs and is available upon request. RNA-seq data processing and pooled CRISPR NGS were conducted using open source software as indicated in the key resources table. Acknowledgments We would like ...
These observations argue for the devel- opment of methods such as CRISPRcleanR, which are in- dependent of CN values for the analysis of CRISPR-KO screening data, and indicate that biased responses are not solely due to the amount of DNA damage and may also be caused by additional factors...
Source data Supplementary Figure 5 A pilot screen to identify optimal conditions for UMI-based CRISPR screen analysis. Setup of screen; Upon editing, various clonal outgrowth regiments, followed by clonal expansion and dropout screening, were run in parallel. Cas9 expression was induced by Dox, ...
Next, we sought to understand how gRNA position within the CDS of the target gene impacts gRNA activity. Given that most gRNAs in Project Achilles were located in the first 50% of the target CDS by design, we obtained a different screening dataset; we downloaded data from a genome-wide fit...