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113 protocols using statplus

1

Statistical Analysis Protocols for Biological Research

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Statistical analyses were performed using Student’s t-test to compare two samples. Statistical analyses comparing more than two groups were performed using a one-way analysis of variance with the StatPlus software program (AnalystSoft Inc., Walnut, CA, USA). Statistical significance was set at P <0.05 for all tests.
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2

Salivary Cortisol and Energy Expenditure

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Raw data were analyzed using a statistical software package (StatPlus, AnalystSoft Inc.—statistical analysis program for Mac OS®. Version v6. See http://www.analystsoft.com/en/). To check the normal distribution of the sampling, a Shapiro-Wilk test was applied. Whether this test failed, a non-parametric approach was applied. In consideration of preliminary results on salivary cortisol, hematological and blood chemistry measurements, and energy expenditure calculation, a sample size of 80 participants was selected to ensure a statistical power higher than 0.80 and a type 1 error of <0.05. Intention to treat approach was utilized to analyze the experimental data: missing values (participants dropout) were considered in the statistical analysis. A two-way (group x time) analysis of variance (ANOVA) was used to establish statistical differences among conditions. When necessary, a Bonferroni post-hoc, with Bonferroni correction test, was used to determine specific differences and interactions among variables A Kruskal Wallis ANOVA on ranks was applied to establish statistical differences among conditions presenting a non-normal distribution. Significance level was set at α<0.05. Results are presented as mean ± standard deviation (SD).
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3

Cytotoxicity, Anti-Proliferation, Apoptosis

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The data from three independent experiments on cytotoxicity, anti-proliferative activity, and apoptosis rate obtained by flow cytometry were used and expressed as means ± SD. Statistical analysis was performed using one-way ANOVA test with Stat-Plus software (AnalystSoft VC 2009, Walnut, CA, USA), with the threshold of significance set at p-value < 0.05.
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4

Kinetochore-Fiber Dynamics Analysis

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Data are reported as mean±SEM and for average traces (Figure 1) data were collected into 8s wide bins before averaging. One-way ANOVA were performed using StatPlus (Version v6; AnalystSoft) to compare between more than two experimental conditions and followed up with two-tailed unpaired Student’s T-tests performed using MatLab, without testing for whether assumptions for normality were met due to low sample sizes. We used p<0.05 as the threshold for statistical significance and indicated in the figure and figure legend if the p-value was lower than 0.05, 0.01 or 0.001 using asterisks (* or ** or *** respectively). ‘n’ always refers to number of kinetochores or kinetochore-fibers except in Figure 2E where ‘n’ refers to number of cells and Figure 2F where ‘n’ refers to the number of timepoints pooled across kinetochores in each experimental condition. Both the number of kinetochores and the number of cells are provided in Table 1 for clarity, but statistical tests were always performed on kinetochore measurements pooled from different cells collected across at least two independent experiments. Sample sizes, statistical tests and p-values are also indicated in the text, figures and figure legends where relevant.
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5

Peptide Identification and Retention Analysis

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All peptides that had a higher Mascot score than 10 were considered. Peptide retention times were determined manually from. RAW files using the apex of the peaks displayed in Xcalibur software (Thermo-Fisher), and resulting MS/MS data were visually inspected for fragmentation that was consistent with peptide assignments. Chromatographic peaks for each peptide had to have a peak asymmetry value of between 0.25 and 4, and peptides exhibiting peak widths greater than 5.5 min were excluded from analysis. Peptide retention times in minutes were converted to glucose units based on dextran samples that were run immediately before. Linear regression analysis using StatPlus (AnalystSoft, Walnut, CA, USA) was used to find the incremental retention coefficients for each amino acid.
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6

Quantifying Gene Expression in Human Corneal Epithelial Cells

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Using Invitrogen High Capacity RNA-to-cDNA Kit (Life Technologies, Grand Island, NY, USA), RNA isolated from cultured HCECs (200 ng per sample) was reverse transcribed into cDNA. cDNA samples were diluted 25-fold to 500 microliters. Quantitative real-time PCR (Q-PCR) was performed using Invitrogen Power SYBR Green Master Mix according to manufacturer’s protocol (Life Technologies). In this study, HCEC cultured for 72 hours and 14 days on 800 nm feature width silk film topographies were compared to HCECs cultured on flat silk and TCP controls (n = 3). The expressions of candidate genes were normalized against glyceraldehyde-3-phosphate-dehydrogenase (GAPDH). Differential expression analysis was performed using the ddCt method22 (link). ANOVA (StatPlus, Version 6, AnalystSoft Inc., Walnut, CA) was used to analyze the statistical significance of Q-PCR data. Test results with P < 0.05 were declared statistically significant.
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7

Quantitative Protein Analysis Protocol

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Data are expressed as means ± SEM. Calculations of p-values (Mann-Whitney U and Wilcoxon Signed-Rank tests) were done in StatPlus (AnalystSoft).
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8

Chronic Hypoxic Rearing Impacts Axin2 Deletion

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Chronic hypoxic rearing was performed as previously described (Weiss et al., Experimental Neurology, 189: pp. 141–149 (2004)). Briefly, C57/B6 litters were culled to a size of 8 pups, cofostered with a CD1 dam and reared from P3 to P11 in a ventilated hypoxia chamber set to 10% 02 (A-Chamber, Biospeherix, Ltd. Lacona, NY). Following hypoxic rearing animals were returned to normal housing, weened at P28, and sacrificed at P40 as were normoxic controls. Statistical significance for the interaction effect of chronic hypoxic rearing and Axin2 deletion was determined by Two-Way ANOVA tests using the StatPlus software plugin (AnalystSoft) for Microsoft Excel. P-values of less than 0.05 are reported as significant.
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9

Comparative Analysis of Biochemical Markers

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Values are the means ± standard deviation (SD) from separate experiments. Intergroup comparisons were made using the unpaired Student’s t-test using Excel (Microsoft, Redmond, WA, USA). A one-way analysis of variance (ANOVA) was followed by a Fisher’s protected least significant difference (PLSD) test as a post hoc comparison using StatPlus (AnalystSoft, Walnut, CA, USA). Differences were considered statistically significant when p < 0.05.
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10

Quantitative Analysis of Protein Expression

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Electron micrographs of the labeled sections were obtained and analyzed in an unbiased manner as described previously (Mednieks et al., 2015 ; Dagdeviren et al., 2018a (link)). Labeling densities of secretory granules of acinar cells, terminal tubule/granular intercalated duct cells, and granular convoluted duct cells were calculated for each mouse as the average number of gold particles/μm2. For direct comparison between different immunogold labeling experiments, the labeling densities were converted to percentages of the corresponding ground control averages. Differences in expression of each protein between the flight and ground control groups were evaluated using ANOVA and t-test functions in Microsoft Excel or StatPlus (v.6.1.60, AnalystSoft, Walnut, CA, USA).
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