Journal: STAR Protocols

Article Title: Analysis workflow of publicly available RNA-sequencing datasets

doi: 10.1016/j.xpro.2021.100478

Figure Lengend Snippet: Gene expression analysis based on SARS-CoV-2 positivity and age Dot plot for MX1 expression (i) and statistical output from RStudio (ii) for: (A) SARS-CoV-2 positive vs . negative patients (P-values correspond to Wilcoxon rank-sum test); (B) SARS-CoV-2 positive vs . negative patients categorized by age groups (P-values correspond to decreasing Jonckheere-Terpstra trend test. Alternative hypothesis: Median i > Median j > … > Median n , indicating that gene expression is significantly lower in SARS-CoV-2 patients when age is increased. Left panel: SARS-CoV-2 negative; right panel: SARS-CoV-2 positive). A.i and B.i were adapted with permission from Bizzotto et al., 2020 .

Article Snippet: Statistical significance: ∗ p < 0.05; ∗∗ p < 0.01; ∗∗∗ p < 0.001. (B) Scatter plot of MX1 and MX2 gene expression levels, color-coded by viral load (i) and Spearman correlation output in RStudio (ii).

Techniques: Gene Expression, Expressing

Journal: STAR Protocols

Article Title: Analysis workflow of publicly available RNA-sequencing datasets

doi: 10.1016/j.xpro.2021.100478

Figure Lengend Snippet: Correlation analysis (A) Pairwise Spearman correlation matrix analysis between all genes of interest ( MX1 , MX2 , ACE2 and TMPRSS2 ), considering different infection status (all patients together (Corr.), SARS-CoV-2 negative (HEALTHY), or SARS-CoV-2 positive patients (COVID19)). Alternative hypothesis: rho (ρ) ≠ 0, which indicates that there is a lineal correlation between the variables under study. Statistical significance: ∗ p < 0.05; ∗∗ p < 0.01; ∗∗∗ p < 0.001. (B) Scatter plot of MX1 and MX2 gene expression levels, color-coded by viral load (i) and Spearman correlation output in RStudio (ii). A and 3B.i were adapted with permission from Bizzotto et al., 2020 .

Article Snippet: Statistical significance: ∗ p < 0.05; ∗∗ p < 0.01; ∗∗∗ p < 0.001. (B) Scatter plot of MX1 and MX2 gene expression levels, color-coded by viral load (i) and Spearman correlation output in RStudio (ii).

Techniques: Infection, Gene Expression

Journal: STAR Protocols

Article Title: Analysis workflow of publicly available RNA-sequencing datasets

doi: 10.1016/j.xpro.2021.100478

Figure Lengend Snippet: Patient segregation based on gene expression (A) Principal component analysis (PCA) output in RStudio, showing the first two principal components explaining most part of the variance among samples. (B) PCA biplot of gene expression data showing a rough segregation of SARS-CoV-2 positive and negative samples. (C) 3D scatter plot for the expression of three genes of interest ( BSG , MX1 and ACE2 ). Samples are colored by SARS-CoV-2 status (positive or negative). Ellipsoids represent the 95% confidence interval. B and 4C were adapted with permission from Bizzotto et al., 2020 .

Article Snippet: Statistical significance: ∗ p < 0.05; ∗∗ p < 0.01; ∗∗∗ p < 0.001. (B) Scatter plot of MX1 and MX2 gene expression levels, color-coded by viral load (i) and Spearman correlation output in RStudio (ii).

Techniques: Gene Expression, Expressing