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111 protocols using prism software v8

1

Statistical Analysis of Cellular Assays

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A two-tailed Student’s t-test was used to compare mean values between sensitive and resistant cells using the following parameters: mean ΔΔCT values for QPCR; mean colony number for soft agar growth assays; mean densitometry values for QPCR and WB; mean percentage of cell viability assay (Cell Titer-Glo) and FACS analysis; mean luminescence for ATP activity in cell growth, Caspase Glow assays in apoptosis measurements; mean tumor weights in xenograft studies. Chi-squared analysis was performed to compare incidences between sensitive and resistant cells for the following assays: number of positive wells containing tumor spheres in the sphere formation assay; numbers of mice developing tumors in xenograft studies. For experiments involving three or more groups, statistical significance was calculated with GraphPad Prism Software v.8 (San Diego, CA, USA) using a 1-way or 2-way ANOVA with a Bonferroni’s posttest, Student’s t test, or log-rank (Mantel-Cox) test where appropriate (GraphPad Prism Software v.8 (San Diego, CA, USA)). Data are represented as the mean ± SD.
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2

Vaccination-Induced Antibody Dynamics

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Results represent the individual result, mean ± SEM of 4–6 mice per group, unless indicated otherwise. Statistical significance was compared between vaccinated groups 1–5 versus PBS (indicated in black as *P < 0.05, **P < 0.01 and ***P < 0.0001) and when relevant and indicated within vaccinated groups (indicated in colour for the comparator group as #P < 0.05, ##P < 0.01 and ###P < 0.0001) using a one‐way ANOVA (unless indicated) on GraphPad Prism Software v8 (San Diego, CA, USA). To compare the endpoint titrations of IgG between groups, the area under the curve (AUC) was calculated for each individual mouse serum and groups AUC was compared using a one‐way ANOVA on GraphPad Prism Software v8. In Figure 6h, the delta change for the AUC at different time points was calculated as follows: delta 1 representing AUC at day 7 post‐challenge – AUC at vaccination time point; and delta 2 representing AUC at day 21 post‐challenge – AUC at day 7 post‐challenge.
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3

Statistical Analysis with GraphPad Prism

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GraphPad Prism Software v8.0.2 (GraphPad, San Diego, CA, USA) was used for statistical analysis. Shapiro–Wilk normality test (α of 0.01) was performed to test for a normal-data distribution. When the normality test was passed, for analysis between couple of conditions an unpaired parametric Student’s t-test was performed; when all conditions were analysed together, an unpaired one-way ANOVA with Tukey post hoc test was used. The level of significance was set at p-value ≤ 0.05, with tendency at 0.1 ≤ p-value < 0.05.
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4

Statistical Analysis and Visualization

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Prism software v. 8.0.2 (GraphPad, USA) was used for statistical analysis and preparation of plot graphs. Statistical significance was determined using the unpaired Student’s t test.
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5

Immuno-phenotyping and Correlation Analysis

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Descriptive statistics were used to summarize the data. Continuous variables are shown as median and IQR. Baseline immuno-phenotyping data were analyzed by one-way ANOVA and post hoc test using the Tukey-Kramer test. The difference between pre- and post-treatment data was assessed using the Wilcoxon signed-rank test. The correlation coefficient was used for matrix correlation analysis. p values less than 0.05 were considered significant. All analyses were conducted using JMP version 14.0 (SAS Institute, Cary, NC, USA) or GraphPad Prism software V.8.0 (GraphPad, La Jolla, CA, USA).
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6

Methyltransferase Enzyme Kinetics Assay

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We dispensed 3 μL of varying substrate ((SPRKIA; 7-points, from 375 nM to 5.0 μM) solution into a 1536-well solid-bottom white plate. To initiate the reaction, a 1 μL enzyme mixture (NTMT1 and SAM at final concentrations of 125 nM (nominal) and 10 μM, respectively) was added to all wells for a final assay volume of 4 μL. The plate was incubated (RT, protected from light) intermittent over a time period of 1 to 120 minutes followed by a 1 μL addition of [5X] MTase-Glo Reagent®. Samples were incubated (RT, protected from light) for 30 minutes, followed by a 2.5 μL addition of [0.5X] MTase-Glo Detection Solution®. The plate was centrifuged for 15 seconds at 1,000 RPM’s, followed by a RT incubation for 30 minutes and detected as described above. The data were fitted to the Michaelis-Menten equation using GraphPad Prism software v8.0 to calculate apparent Km values.
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7

Cytotoxicity Assay of Mammalian and Insect Cells

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Viability of mammalian Vero and insect KC cells was measured using the MTT Cell Proliferation and Cytotoxicity Assay Kit (Boster Biological Technology, Pleasanton, CA 9, USA) following the manufacturer’s instructions. Briefly, confluent cells (96-well plate format, 5 × 104 cells/well, triplicates) were treated with 100 μL of medium containing the indicated concentrations of ATA (two-fold dilutions, starting concentration of 1000 μM). Plates were incubated at 37 °C or 29 °C for 24 h. Samples were treated with 15 μL of Dye Solution and incubated at 37 °C in a 5% CO2 atmosphere for 5 h. Next, the cells were treated with 100 μL of Formazan solubilisation solution for 16 h, and absorbance at 570 nm was read using a microplate reader. The viability of compound-treated cells was calculated as a percentage relative to values obtained with mock-treated cells. Non-linear regression curves and the median cytotoxic concentration (CC50) were calculated using GraphPad Prism software v. 8.0. (GraphPad Software, San Diego, CA, USA).
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8

Statistical Analysis of Experimental Data

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Data are presented as individual data points with summary statistics (median ± IQR or mean ± SD) according to whether data are normally distributed. Parametric or nonparametric statistical tests were applied as appropriate after data were tested for normality using the Kolmogorov-Smirnov test. Tests used for comparisons are indicated in figure legends. Two-tailed P values were computed; a P value of less than 0.05 was considered statistically significant. Statistical analyses were undertaken using GraphPad Prism Software v8.0.
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9

Neutralizing Antibody Titer Assay for SFTSV

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To assess the neutralizing efficacy of sera from immunized mice, a 50% focus reduction neutralization titer (FRNT50) assay was utilized. Sera were first inactivated by heating at 56°C for 30 min and then diluted four-fold across four points, ranging from 1:40 to 1:2560. Each serum dilution was mixed and incubated with an equal volume of SFTSV solution (containing 100 FFU) at 4°C for 1 h. This inoculated mixture was then applied to a monolayer of VeroE6 cells housed in a 24-well plate (SPL Life Sciences, Pocheon, Republic of Korea) and incubated for 2 h at 37°C. After this period, supernatants were discarded, and cells were cultured in an overlay medium (DMEM supplemented with 2% FBS, 1% penicillin/streptomycin, and 1% methylcellulose) at 37°C for 6 days. The process for visualizing viral foci is as described above. Percentage focus reduction was calculated as [(No. of plaques without antibodies) − (No. of plaques with antibodies)]/(No. of plaques without antibodies) × 100. All the experiments were duplicated and the FRNT50 was calculated using nonlinear regression analysis (log[inhibitor] versus normalized response method) embedded in GraphPad Prism Software v8.0 (GraphPad Software; https://www.graphpad.com). All FRNT50 assays were conducted alongside negative control sera to establish the limit of detection under our experimental conditions.
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10

Prognostic Factors in Relapse-Free Survival

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The results are presented as the mean ± standard deviation, and the Mann-Whitney U test, Wilcoxon signed-rank test, and a Spearman correlation analysis were used in this study. Relapse-free survival (RFS) was determined using the Kaplan-Meier method. A 2-tailed P value of <0.05 was considered statistically significant in this study. Multivariate analysis was done using Cox regression analysis after adjusting for other prognostic factors (P value <0.05 was considered significant). All the statistical analyses were conducted using IBM SPSS Statistics V.25.0, R V.3.5.1, and GraphPad Prism Software V.8.0.
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