Computational protocol: MERTK as a novel therapeutic target in head and neck cancer

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Protocol publication

[…] Cell cycle was analyzed using propidium iodide (PI) staining. Cells were treated with increasing amounts of UNC1062 and were harvested after different time points. Similarly MERTK knockdown cells were harvested 72 hours after induction with doxycycline. Cells were washed two times with sample buffer (0.1 % glucose (Merck, Darmstadt, Germany) in PBS), fixed with ice-cold 70 % ethanol (AppliChem, Darmstadt, Germany) for at least 24 hours at 4°C. Staining was performed with PI staining solution (Sample buffer with 50 μg/ml PI (Sigma-Aldrich, München, Germany) and 50 μg/ml RNAse A (Life technologies, Darmstadt, Germany) for 30 minutes at room temperature before flow cytometry analysis (BD FACSCantoTM II, BD Biosciences, Heidelberg, Germany). Data was evaluated using FlowJo Software (Tree Star, Ashland, OR, USA). [...] Differences of continuous variables between two groups were tested at a two-sided significance level of 0.05 with Students t-Test for normally distributed data or non-parametric Mann-Whitney U test otherwise and the Kruskal-Wallis-H for more than two nominal categories. Significance of monotonic trends in ordinal variables was evaluated with the non-parametric Jonckheere-Terpstra test. P-values for independence of categories in contingency tables was calculated using the Fisher exact test for small to medium sample sizes and Fisher test with 100 000 random Monte Carlo simulations for large sample sizes. Survival was analyzed using Kaplan-Meier estimators with log-rank test and Cox regression models with adjustment for clinical co-variables [, ]. All statistical analyses were performed using R software package [] and IBM SPSS Statistics 22. […]

Pipeline specifications

Software tools FlowJo, SPSS
Applications Miscellaneous, Flow cytometry
Organisms Homo sapiens
Diseases Head and Neck Neoplasms, Neoplasms