Journal: eLife

Article Title: Endogenous tagging using split mNeonGreen in human iPSCs for live imaging studies

doi: 10.7554/eLife.92819

Figure Lengend Snippet:

Article Snippet: Chemical compound, drug , NU7441 , Tocris Bioscience , 3712 , NHEJ inhibitor.

Techniques: Recombinant, Sequencing, Ligation, Digital PCR, Software, Polymer, Imaging

Journal: Disease Models & Mechanisms

Article Title: CRISPR/Cas9-mediated homology-directed repair by ssODNs in zebrafish induces complex mutational patterns resulting from genomic integration of repair-template fragments

doi: 10.1242/dmm.035352

Figure Lengend Snippet: Influence of chemical compound administration through injection on HDR efficiency. Injection mixes containing the NT 120 S repair template were complemented with chemical compounds that either inhibit specific components of the NHEJ pathway, including SCR7, NU7441 and KU0060648, or that were shown to stimulate the HDR pathway, including RS1 and L755507. Five independent experiments were carried out and average total HDR rates are shown, split into two categories: perfect repair % (plain bars) and erroneous repair % (dashed bars). Error bars represent the s.e.m. for five independent biological replicates each consisting of a pooled sample of 20 embryos. Repair rates depicted in this graph are listed in Table S4 . Statistical tests performed: independent samples t -test for normal distributed groups and the non-parametric independent samples Mann–Whitney U -test for non-normal distributed groups.

Article Snippet: The following chemical compounds were dissolved in DMSO and either supplemented to the injection mix ( Table S9 ) or to the compound screening medium ( Table S10 ): SCR7 (Xcessbio Biosciences Inc., cat. no. M60082-2s), KU0060648 (APExBIO, cat. no. A1769), NU7441 (Santa Cruz Biotechnology, cat. no. sc-208107), L755507 (Santa Cruz Biotechnology, cat. no. sc-204045), RS1 (Santa Cruz Biotechnology, cat. no. sc-222240).

Techniques: Injection, MANN-WHITNEY

Journal: Frontiers in Immunology

Article Title: DNA-PKcs restricts Zika virus spreading and is required for effective antiviral response

doi: 10.3389/fimmu.2022.1042463

Figure Lengend Snippet: DNA-PKcs is critical for control of ZIKV infection. Virus replication measured by plaque assay, expressed as plaque-forming units per mL (PFU/mL), on (A) A549 WT and A549 PRKDC-/- or (B) RPE WT and RPE PRKDC-/- cells infected with ZIKV at indicated m.o.i. and time. RT-qPCR analysis to measure ZIKV RNA in (C) A549 WT and A549 PRKDC-/- or (D) RPE WT and RPE PRKDC-/- cells infected at indicated m.o.i. and time. (E) A549 WT and A549 PRKDC-/- or (F) RPE WT and RPE PRKDC-/- cells infected with 50 PFU of ZIKV at 48 hours in semi-solid medium, then ZIKV-E protein (green) was stained for immunofluorescence analysis, and the relative area of infection percentage was measured using the ImageJ software. The cell nuclei were stained with DAPI (blue). (G) Percentage of ZIKV-infected A549 WT and A549 PRKDC-/- cells at indicated m.o.i. and time, analyzed by flow cytometry. (H) Viability analysis by MTT assay of ZIKV-infected A549 WT and A549 PRKDC-/- cells relative to uninfected cells (mock) at indicated m.o.i. and time. (I) A549 WT and A549 PRKDC-/- were pretreated with NU7441 (0.5 and 1 µM) at 24 hours followed by ZIKV infection (m.o.i. 1) at 24 hours. We used two-way ANOVA with Sidak’s correction in (A–D, G, H) , and unpaired two-tailed Student’s t-test was used in (E, F) . * p<0.05, n = 3, error bars ± SEM.

Article Snippet: Cells were treated with 0.5 or 1 μM of NU7441 (BioGems, 5039598), 100 ng/mL human TNF (Peprotech, 300-01A), and 3 μM etoposide (Sigma, E1383).

Techniques: Control, Infection, Virus, Plaque Assay, Quantitative RT-PCR, Staining, Immunofluorescence, Software, Flow Cytometry, MTT Assay, Two Tailed Test

Journal: Frontiers in Immunology

Article Title: DNA-PKcs restricts Zika virus spreading and is required for effective antiviral response

doi: 10.3389/fimmu.2022.1042463

Figure Lengend Snippet: ZIKV infection does not induce DSB in A549 cells. A549 WT , A549 PRKDC-/- and 1 µM NU7441 pre-treated A549 WT infected with ZIKV (m.o.i. 1) at 24 hours. Stimulation with 3 µM etoposide for 12 hours was used as a DSB positive control. (A) Immunofluorescence to analyze γH2AX (green) in the ZIKV-infected cells (red, ZIKV-E protein). The cell nuclei were stained with DAPI (blue). (B) Percentage of γH2AX foci per cell showed in (A) . *Compared with WT cells; #Compared with mock. We used two-way ANOVA with Sidak’s correction. * or # p<0.05, n = 3, error bars ± SEM.

Article Snippet: Cells were treated with 0.5 or 1 μM of NU7441 (BioGems, 5039598), 100 ng/mL human TNF (Peprotech, 300-01A), and 3 μM etoposide (Sigma, E1383).

Techniques: Infection, Positive Control, Immunofluorescence, Staining