Journal: Molecular Therapy. Nucleic Acids

Article Title: Extracellular vesicle microRNA and protein cargo profiling in three clinical-grade stem cell products reveals key functional pathways

doi: 10.1016/j.omtn.2023.03.001

Figure Lengend Snippet: Differential expression of microRNAs from EVs Differential expression analysis of miRNAs between cell types was performed using ROSALIND t test method. p value adjustment was performed using the Benjamini-Hochberg method of estimating false discovery rates (FDRs). miRNAs were considered differentially expressed with a log2 fold change ≥ or ≤1.5 and p <0.05. Log2 fold change and p values were exported from ROSALIND to construct volcano plots and heatmaps using GraphPad Prism v.9.1 and RStudio (pheatmap package), respectively. (A) Volcano plot showing 20 downregulated and 36 upregulated miRNA transcripts, and heatmap showing the significant differentially expressed miRNAs in HDC vs. BM-MSC EVs. (B) Volcano plot showing 12 downregulated and 164 upregulated miRNA transcripts, and heatmap showing the significant differentially expressed miRNAs in BM-MSC vs. UC-MSC EVs. (C) Volcano plot showing 15 downregulated and 299 upregulated miRNA transcripts, and heatmap showing the significant differentially expressed miRNAs in HDC vs. UC-MSC EVs. The list of differentially expressed miRNAs is provided in Tables S1 , , and . n = 3 biological replicates. BM-MSC, bone marrow-derived mesenchymal stromal cells; HDC, heart-derived cells; UC-MSC, umbilical cord-derived mesenchymal stromal cells.

Article Snippet: Log2 fold changes, p values, and normalized log2 count data were exported from ROSALIND to construct volcano plots and heatmaps using GraphPad Prism v.9.1 and RStudio (pheatmap package), respectively. miRNA functional enrichment analysis was analyzed using TAM 2.0 ( http://www.lirmed.com )., The list of mature miRNA names from the normalized ROSALIND data was used as input (overrepresentation, p ≤ 0.05).

Techniques: Quantitative Proteomics, Construct, Derivative Assay

Journal: Molecular Therapy. Nucleic Acids

Article Title: Extracellular vesicle microRNA and protein cargo profiling in three clinical-grade stem cell products reveals key functional pathways

doi: 10.1016/j.omtn.2023.03.001

Figure Lengend Snippet: Differential expression of proteins from EVs Differential expression analysis of proteins between cell types was performed using Perseus ( https://maxquant.net/perseus/ ). Proteins identified in at least 2 of 3 replicates were considered for analysis. Two-sample two-tailed Student’s t test with permutation-based FDR (FDR = 0.05, no. of randomizations = 250) was used to calculate statistical significance between cell types. The proteins were considered differentially expressed with a p <0.05. Log2 difference and p values were exported from Perseus to construct volcano plots and heatmaps using GraphPad Prism v.9.1 and RStudio (pheatmap package), respectively. (A) Volcano plot showing 9 downregulated and 14 upregulated proteins, and heatmap showing the significant differentially expressed proteins in HDC vs. BM-MSC EVs. (B) Volcano plot showing 198 downregulated and 107 upregulated proteins, and heatmap showing the significant differentially expressed proteins in BM-MSC vs. UC-MSC EVs. (C) Volcano plot showing 141 downregulated and 119 upregulated proteins, and heatmap showing the significant differentially expressed proteins in HDC vs. UC-MSC EVs. The list of differentially expressed proteins is provided in Tables S4 , , and . n = 3 biological replicates. BM-MSC, bone marrow-derived mesenchymal stromal cells; HDC, heart-derived cells; UC-MSC, umbilical cord-derived mesenchymal stromal cells.

Article Snippet: Log2 fold changes, p values, and normalized log2 count data were exported from ROSALIND to construct volcano plots and heatmaps using GraphPad Prism v.9.1 and RStudio (pheatmap package), respectively. miRNA functional enrichment analysis was analyzed using TAM 2.0 ( http://www.lirmed.com )., The list of mature miRNA names from the normalized ROSALIND data was used as input (overrepresentation, p ≤ 0.05).

Techniques: Quantitative Proteomics, Two Tailed Test, Construct, Derivative Assay

Journal: Nature Communications

Article Title: Natural variation of an E3 ubiquitin ligase encoding gene Chalk9 regulates grain chalkiness in rice

doi: 10.1038/s41467-025-61683-4

Figure Lengend Snippet: a The genome-wide association signals for chalky grain rate (CGR) and degree of chalkiness (DC) in the region at 18–21 Mb on chromosome 9 ( x -axis) across two years. Negative log 10 -transformed P values from the linear mixed model are plotted on the y -axis. The horizontal dashed line indicates the genome-wide significance threshold ( P = 1×10 –6 ). P values were determined using a two-sided Wald test and assessed after Bonferroni correction for multiple comparisons. b Linkage disequilibrium (LD) heatmap of the Chalk9 locus region. Pairwise linkage disequilibrium was determined by calculating r 2 (the square of the correlation coefficient between SNPs). c Relative expression level of the 12 candidate genes in the endosperm of eight high-chalky and eight low-chalky varieties at 20 days after flowering (DAF). The 12 predicted genes in the Chalk9 locus region are labeled by I to XII. Data show means ± SD ( n = 8 varieties). P values were calculated for comparisons between high-chalky and low-chalky groups, with each group comprising 8 varieties. d Relative expression level of the candidate gene III ( Chalk9 ) in the endosperm from the selected varieties at 20 DAF. The P value was calculated for the comparison between high-chalky and low-chalky groups, with each group comprising 8 varieties. Data show means ± SD ( n = 3 biological replicates). e Relative expression level of the 12 candidate genes in the leaves of eight high-chalky and eight low-chalky varieties. Data show means ± SD ( n = 8 varieties). In c – e , statistical analysis between high-chalky and low-chalky groups was performed by two-tailed Student’s t -test. Source data are provided as a Source Data file.

Article Snippet: Correlation analysis, heatmap plotting, and volcano plot analysis were performed using BMKCloud ( www.biocloud.net ).

Techniques: GWAS, Transformation Assay, Genome Wide, Expressing, Labeling, Comparison, Two Tailed Test

Journal: Emerging Microbes & Infections

Article Title: Elevated pulmonary tuberculosis biomarker miR-423-5p plays critical role in the occurrence of active TB by inhibiting autophagosome-lysosome fusion

doi: 10.1080/22221751.2019.1590129

Figure Lengend Snippet: A potential TB diagnostic model was established when combined miR-423-5p, miR-17-5p and miR-20b-5p as a panel. (A) The levels of four serum miRNAs were measured by qPCR from TB patients ( N = 70) and healthy controls (HCs, N = 51). Median values are shown by horizontal lines. (B) The Receiver Operating Characteristic curve of miR-17-5p, miR-20b-5p, miR-423-5p and the combined model were analyzed. N: number of subjects. * P < 0.05, ** P < 0.01, *** P < 0.001.

Article Snippet: The Volcano Plot of the differentially expressed serum miRNAs was performed by GraphPad Prism 5.

Techniques: Diagnostic Assay