Genome-wide astrocyte fidelity scores were obtained from Kelley et al. TPM: transcripts per million. b, Relative expression (z-scored) of the top 50 genes with the highest astrocyte fidelity scores from Kelley et al.115 (organized by hierarchical clustering, see Methods) in iAstrocytes vs. ...
To enable gain-of-function and loss-of-function arrayed CRISPR screens, we generated genome-wide activation (‘T.gonfio’, meaning swelling up) and deletion (‘T.spiezzo’, meaning breaking in two) arrayed libraries for human protein-coding genes using ALPA cloning (Fig. 1e). We used the...
Improved vectors and genome-wide libraries for CRISPR screening Nat Methods, 11 (8) (2014), pp. 783-784, 10.1038/nmeth.3047 View in ScopusGoogle Scholar Shyian et al., 2016 M. Shyian, S. Mattarocci, B. Albert, L. Hafner, A. Lezaja, M. Costanzo, C. Boone, D. Shore Budding yea...
Genome-wide functional screening using the CRISPR-Cas9 system is a powerful tool to uncover tumor-specific and common genetic dependencies across cancer cell lines. Current CRISPR-Cas9 knockout libraries, however, primarily target protein-coding genes. This limits functional genomics-based investigations ...
Genome-wide CRISPR/Cas9 knockout screens in the K562 cell line. (a) Required cell number for H-mLibA, H-mLibB, and Brunello libraries screening. To reach a 500 × coverage screening experiment, H-mLibA and H-mLibB require approximately 11 million cells while Brunello requires approximat...
Genome-wide functional screening using the CRISPR-Cas9 system is a powerful tool to uncover tumor-specific and common genetic dependencies across cancer cell lines. Current CRISPR-Cas9 knockout libraries, however, primarily target protein-coding genes. T
Human papillomavirus (HPV) drives almost all cervical cancers and up to 70% of head and neck cancers. Frequent integration into the host genome occurs predominantly in tumorigenic types of HPV. We hypothesize that changes in chromatin state at the l
Data were filtered manually according to common quality-control metrics (i.e., the number of unique genes detected in each cell, the total number of RNA molecules detected in each cell, and the percentage of reads that mapping to the mitochondrial genome) with Seurat.104 We performed cell-...
Thus, it is imperative to analyze the on/off status and c-JUN binding status of relevant genes during differentiation from the perspective of genome accessibility. To achieve this, we conducted ATAC-seq, a method for mapping chromatin accessibility genome-wide [50, 51]. Our analysis of ThO ...
Genome engineering using CRISPR/Cas9 technology enables simple, efficient and precise genomic modifications in human cells. Conventional immortalized cell lines can be easily edited or screened using genome-wide libraries with lentiviral transduction. However, cell types derived from the differentiation of ...