Journal: Cell Reports

Article Title: Genome-wide Screens Implicate Loss of Cullin Ring Ligase 3 in Persistent Proliferation and Genome Instability in TP53 -Deficient Cells

doi: 10.1016/j.celrep.2020.03.029

Figure Lengend Snippet:

Article Snippet: gRNA pooled library in lentiCRISPRv2 (gift from Feng Zhang) , Addgene , Cat#1000000048.

Techniques: Recombinant, Ligation, Viability Assay, Sequencing, Plasmid Preparation, Software, Infection, Transfection, Staining

Journal: Cell Research

Article Title: Three-dimensional bioprinted glioblastoma microenvironments model cellular dependencies and immune interactions

doi: 10.1038/s41422-020-0338-1

Figure Lengend Snippet: a Schematic diagram of whole-genome CRISPR-Cas9 loss-of-function screening strategy in standard sphere culture conditions and the 3D tetra-culture model. b PCA of functional dependencies defined by whole genome CRISPR-Cas9 screening as defined in ( a ). c Volcano plot demonstrating genes that enhance (blue) or inhibit (red) cell proliferation in sphere culture when inactivated by a specific sgRNA in a whole genome CRISPR-Cas9 loss-of-function screen. The x-axis displays the Z-score and the y-axis displays the P value as calculated by the MAGECK-VISPR algorithm. d Volcano plot demonstrating genes that enhance (blue) or inhibit (red) cell proliferation in the 3D tetra-culture model when inactivated by a specific sgRNA in a whole genome CRISPR-Cas9 loss-of-function screen. The x-axis displays the Z-score and the y-axis displays the P value as calculated by the MAGECK-VISPR algorithm. e Pathway gene set enrichment connectivity diagram displaying pathways enriched among functional dependency genes common to both sphere culture and 3D culture in the tetra-culture model. f Plot comparing the functional dependency Z-scores between sphere culture and 3D culture in the tetra-culture model. g Pathway gene set enrichment connectivity diagram displaying pathways enriched among functional dependency genes that are specific to sphere culture, as defined in f . h Pathway gene set enrichment connectivity diagram displaying pathways enriched among functional dependency genes that are specific to growth in the 3D tetra-culture, as defined in f . i Volcano plot displaying differential functional dependency scores between sphere culture and the 3D tetra-culture system as defined by MAGECK-VISPR. j Pathway gene set enrichment connectivity diagram displaying pathways enriched among functional dependency genes that are more essential in sphere culture compared to in the 3D tetra-culture system, as defined in i . k Pathway gene set enrichment connectivity diagram displaying pathways enriched among functional dependency genes that are more essential in the 3D tetra-culture system compared to in sphere culture, as defined in i .

Article Snippet: For unlabeled cells, sgRNAs were cloned into the LentiCRISPRV2 plasmid containing a puromycin selection marker (Addgene Plasmid #52961), while luciferase-labeled cells were edited with sgRNAs cloned into the LentiCRISPRV2 plasmid containing a hygromycin selection marker (Addgene Plasmid #98291). sgRNA sequences were chosen from the Human CRISPR Knockout Pooled Library (Brunello) (Supplementary information, Table ).

Techniques: CRISPR, Functional Assay