pearson correlation matrix (pcm) heatmap  (RStudio)

Journal: RNA Biology

Article Title: Distinct small non-coding RNA landscape in the axons and released extracellular vesicles of developing primary cortical neurons and the axoplasm of adult nerves

doi: 10.1080/15476286.2021.2000792

Figure Lengend Snippet: Differentially expressed non-coding RNA genes and analysis of inequality/heterogeneity of the RNA repertoire. (A) Heatmap of differentially expressed genes; 379 DEGs (miRNAs, tRNAs, snoRNAs/scaRNAs and piRNAs), FDR ≤ 0.01 and absolute log2(FC) ≥ 1) for the different samples, with expression shown as Z-score of log2 normalized counts (two-way hierarchical clustering distance measured by Euclidean and Ward clustering algorithms). (B) Bar plot for the number of specific RNAs that make 80% of the total normalized read counts for each of the RNA biotypes in the different samples (mean ± s.e.m.). Bar plot of the (C) Evenness factors and (D) Gini coefficients, reflecting the inequality of abundance distribution of the indicated RNA biotypes in the neuronal and EV compartments. Higher evenness factors or lower Gini coefficients correspond to lower inequality. (E) Analysis of heterogeneity of the sncRNA repertoire between samples. For each RNA biotype, a sum of squared errors (χ2 value) was calculated among samples, after normalization. The χ2 value of EV and AX samples was compared to the WC samples. Fold change of χ2 values higher than 1 reflects the increased heterogeneity. Two-way ANOVA with Tukey’s multiple comparison post-hoc test, * p-value < 0.05; ** p-value < 0.01. Whole Cell (WC), Axon (AX) and Extracellular Vesicles (EV).

Article Snippet: The complete count list was log2 transformed and Heatmap of Pearson correlation was performed using corrplot, gplots and RColorBrewer libraries; and PCA analysis was performed using rgl and plot3d libraries in RStudio ( http://www.rstudio.com/ ).

Techniques: Expressing, Comparison

Journal: RNA Biology

Article Title: Distinct small non-coding RNA landscape in the axons and released extracellular vesicles of developing primary cortical neurons and the axoplasm of adult nerves

doi: 10.1080/15476286.2021.2000792

Figure Lengend Snippet: Characterization of miRNAs in neuronal subcellular and extracellular compartments and selective assessment of axonal growth effects. (A) Relative read abundance of miRNAs in WC, AX and EVs showing the most expressed miRNAs in each neuronal and EV compartment (percentage of the average normalized miRNA counts for each compartment). (C) Heatmap of the differential expression of miRNAs (67 DEGs, FDR ≤ 0.01 and absolute log2(FC) ≥ 1) for the different samples, shown as Z-score of log2 normalized counts (two-way hierarchical clustering distance measured by Euclidean and Ward clustering algorithms). Whole Cell (WC), Axon (AX) and Extracellular Vesicles (EV). (C) Overview of the experimental design for analysis of axonal outgrowth after inhibition of selected axonal miRNAs (D) Representative images of neurons measured after co-transfection with GFP and a specific miR-434-3p inhibitor or non-targeting control (scale bar: 100um). (E) Quantification of axon length in cortical neurons after specific inhibition of miR-434-3p, miR-151-3p and miR-92a showing a decrease in axon length, whereas inhibition of miR-16-5p results in an increase in length of cortical axons. Data presented as % of control expressed in mean±s.e.m, n = 3–6 independent experiments. Student’s t-test, *p-value <0.05.

Article Snippet: The complete count list was log2 transformed and Heatmap of Pearson correlation was performed using corrplot, gplots and RColorBrewer libraries; and PCA analysis was performed using rgl and plot3d libraries in RStudio ( http://www.rstudio.com/ ).

Techniques: Quantitative Proteomics, Inhibition, Cotransfection, Control

Journal: RNA Biology

Article Title: Distinct small non-coding RNA landscape in the axons and released extracellular vesicles of developing primary cortical neurons and the axoplasm of adult nerves

doi: 10.1080/15476286.2021.2000792

Figure Lengend Snippet: tRNA repertoire in the neuronal subcellular and extracellular compartments. (A) Diagrammatic representation of the biogenesis of tRNA-derived small RNAs (tsRNAs), where mature tRNAs undergo endonuclease cleavage to generate tRNA-derived fragments (3ʹ- and 5ʹ- tRFs) and tRNA halves (3ʹ- and 5ʹ- tRHs). (B) Relative read abundance of parental tRNAs upon tsRNAs mapping in WC, AX and EV shows the most expressed tRNA species in each neuronal compartment (percentage of total tRNA reads). (C) Read length (nt) distribution plot for all tsRNAs (mean±s.e.m.), showing a higher frequency of 33nt long reads in all three of WC, AX and EV samples, but an additional 30nt peak that is predominant in EV samples. (D) Percentage distribution of total reads mapping to each class of tsRNAs in all samples following the unitas annotation workflow (mean ± s.e.m). Comparisons between neuronal compartments demonstrate that 5ʹ-tRHs are the most abundant tsRNAs in all samples and represent a significant higher proportion of AX and EV tsRNAs (~90%) compared to WC (70%). (E) Heatmap of the abundance distribution of tsRNAs present in all WC, AX and EV samples. Data expressed as percentage of total reads per tsRNA class. Highlighted in red are the parental tRNAs generating the most abundant 5ʹ-tRHs: 5ʹ-tRHs-Gly-GCC, 5ʹ-tRHs-Val-AAC, 5ʹ-tRHs-Val-CAC and 5ʹ-tRHs-Glu-CTC. Two-way ANOVA with Tukey’s multiple comparison post-hoc test, * p-value < 0.05; ** p-value < 0.01. Whole Cell (WC), Axon (AX) and Extracellular Vesicles (EV).

Article Snippet: The complete count list was log2 transformed and Heatmap of Pearson correlation was performed using corrplot, gplots and RColorBrewer libraries; and PCA analysis was performed using rgl and plot3d libraries in RStudio ( http://www.rstudio.com/ ).

Techniques: Derivative Assay, Comparison

Journal: RNA Biology

Article Title: Distinct small non-coding RNA landscape in the axons and released extracellular vesicles of developing primary cortical neurons and the axoplasm of adult nerves

doi: 10.1080/15476286.2021.2000792

Figure Lengend Snippet: sncRNA profiling of the axoplasm from adult axons. (A) Relative read abundance of each sncRNA biotype in the peripheral nerve’s axoplasm (percentage of total sncRNA reads). (B) Read length (nt) distribution plot of reads mapping to miRNAs, tRNAs, sno/snRNAs (sRNAs) and rRNAs. (C) Relative read abundance of specific miRNAs showing the most expressed in axoplasm samples. Data expressed as percentage of total miRNA reads. (D) Venn diagram illustrates the very high overlap of individual miRNAs detected in the in vivo rat axoplasm (miRNAs ≥ 5 reads) and the in vitro mouse axons (miRNAs ≥ 50 CPM, which is equivalent to ≥ 10 reads). To compare miRNAs of different species only the precursor’s base identification was considered in each case. (E) Venn diagram displaying the overlap of miRNAs detected in our two axon sncRNA-seq datasets ( in vivo rat axoplasm and mouse in vitro axons) and the three currently available RNA-seq axon datasets, in vitro rat motor axon, frog retinal ganglion cells axons and rat sciatic nerves. As above, only the precursor’s base identification was considered in each case. This analysis reveals a core of 23 axonal miRNAs present across all neuronal types, both in in vivo and in vitro axons. (F) Relative read abundance of parental tRNAs shows the most expressed parental tRNA species in axoplasm. Data expressed as percentage of total tRNA reads. (G) Percentage distribution of total reads mapping to each class of tRNA-derived small RNA (tsRNAs), following the unitas annotation workflow (mean ± s.e.m). (H) Heatmap of the distribution of each tsRNA class present in the axoplasm with at least 1% of relative abundance. Data expressed as percentage of total reads from tsRNA class. (I) Relative read abundance of parental sno/scaRNAs and snRNAs shows the most expressed in axoplasm samples. Data expressed as percentage of total sno/scaRNAs and snRNAs reads. (J) Percentage distribution of total reads mapping to each class of sRNAs (snoRNAs/scaRNAs/snRNAs) investigated in axoplasm samples (mean ± s.e.m.).

Article Snippet: The complete count list was log2 transformed and Heatmap of Pearson correlation was performed using corrplot, gplots and RColorBrewer libraries; and PCA analysis was performed using rgl and plot3d libraries in RStudio ( http://www.rstudio.com/ ).

Techniques: In Vivo, In Vitro, RNA Sequencing, Derivative Assay

Journal: Environmental Science and Pollution Research International

Article Title: Air quality assessment among populous sites of major metropolitan cities in India during COVID-19 pandemic confinement

doi: 10.1007/s11356-020-11061-y

Figure Lengend Snippet: Pearson’s correlation heatmap for air pollutants during the pre and COVID-19 pandemic confinement, 2020 among populous sites of four major metropolitan cities in India

Article Snippet: Pearson’s correlation heatmap for Manali Village, Chennai demonstrates significant positive correlations for PM2.5 (0.69) and PM10 (0.73) with AQI, while other pollutants exhibit a moderate or negative correlation.

Techniques: