Journal: International Journal of Molecular Sciences

Article Title: MiR-30a-5p Inhibits Epithelial-to-Mesenchymal Transition and Upregulates Expression of Tight Junction Protein Claudin-5 in Human Upper Tract Urothelial Carcinoma Cells

doi: 10.3390/ijms18081826

Figure Lengend Snippet: Expression profiles of miRNAs in human UTUC tumor and non-tumor samples. Three tumor (T1–T3; light blue to navy blue) and three adjacent normal tissues (N1–N3; orange-yellow-green) were subjected to RNA extraction and NGS-miRNA sequencing through the Illumina MiSeq platform. ( A ) Heat-map clustering analysis was conducted to examine the overall miRNA expression profiles among samples. A line scatterplot was used to present miRNA expression profiles; ( B ) Downregulation of miR-30a-5p in UTUC tumor tissues ( n = 22) compared with adjacent normal controls ( n = 14) by RT-qPCR analysis. The asterisk denotes p < 0.001 using an unpaired t -test.

Article Snippet: The small RNA library construction and deep sequencing was carried out at a Biotechnology Company (Welgene, Taipei, Taiwan).

Techniques: Expressing, RNA Extraction, Sequencing, Quantitative RT-PCR

Journal: BMC Medicine

Article Title: Atorvastatin-pretreated mesenchymal stem cell-derived extracellular vesicles promote cardiac repair after myocardial infarction via shifting macrophage polarization by targeting microRNA-139-3p/Stat1 pathway

doi: 10.1186/s12916-023-02778-x

Figure Lengend Snippet: Small RNA sequencing analysis identifies miR-139-3p as an extracellular vesicle miRNA candidate. A , B Hierarchical clustering heat map ( A ) and volcano plot ( B ) showing 9 differentially expressed miRNAs between MSC-EV and MSC ATV –EV. C Verification for the mRNA expressions in MSC-EV and MSC ATV –EV by qPCR analysis, n = 3–4 per group. * P < 0.05, ** P < 0.01, *** P < 0.001. D , E GO ( D ) and KEGG ( E ) enrichment analysis of target genes of three upregulated miRNAs (miR-139-3p, miR-320-3p, miR-501-3p) between MSC-EV and MSC ATV –EV. F Interaction network between target genes of three upregulated miRNAs (miR-139-3p, miR-320-3p, miR-501-3p) and upregulated genes in patients suffered from first acute myocardial infarction (GEO: GSE24591). G Interaction network between target genes of three upregulated miRNAs (miR-139-3p, miR-320-3p, miR-501-3p) and downregulated genes in human monocyte-derived M2 macrophages (GEO: GSE32164). H The intersection between the three upregulated miRNAs of miR-139-3p, miR-320-3p, miR-501-3p, and 25 downregulated miRNAs in patients suffered from first acute myocardial infarction (GEO: GSE24591) is miR-139-3p. ATV, atorvastatin; EV, extracellular vesicle; GEO, gene expression omnibus; GO, gene ontology; KEGG, Kyoto Encyclopedia of Genes and Genomes; MSCs, mesenchymal stem cells; miRNA, micro-RNA; qPCR, quantitative polymerase chain reaction

Article Snippet: The isolation of total RNA in the EVs, small RNA library construction, and EV small RNA sequencing were conducted by RiboBio Company (Guangzhou, China).

Techniques: RNA Sequencing Assay, Derivative Assay, Expressing, Real-time Polymerase Chain Reaction

Journal: bioRxiv

Article Title: Defining cell type-specific immune responses in a mouse model of allergic contact dermatitis by single-cell transcriptomics

doi: 10.1101/2024.01.16.575925

Figure Lengend Snippet: Characterization of mouse allergic skin immune response by single cell RNA transcriptomic analysis (A) Overview of the experimental setting. Allergic contact dermatitis (ACD)-like skin inflammation was triggered by sequential sensitization and elicitation of ACD by topical application of 1% or 0.2% DNFB on dorsal or ear skin as indicated. Ear skin was collected at 60 hours post-elicitation for analyses. (B) tSNE plots showing the distribution of various cell clusters marked by a color code. (C) Bubble plots showing the expression of marker genes for each cell cluster. Abbreviations: dFB , dermal fibroblast; MC , mast cell; MAC , macrophage; BF , basophil; NEU , neutrophil; VSMC , vascular smooth muscle cell; PC , pericytes; KC , keratinocyte; EC , endothelial cell; SC , Schwann cell. (D) tSNE plots showing how cells were differentially distributed in control and ACD skin samples. Red lines circle key immune cell populations. (E) Stacked bar graph showing the percentage of each cell cluster in the control and ACD samples. (F) qRT-PCR analysis showing the expression of indicated genes (n=4∼6/group). (G) Violin plots showing the expression of indicated genes in the control and ACD samples. Figure supplement 1 . Establishment of the DNFB-elicited ACD mouse model.

Article Snippet: Single cell RNA libraries construction, sequencing and bioinformatic analysis was assisted by GENE DENOVO Inc (Guangzhou, China).

Techniques: Expressing, Marker, Quantitative RT-PCR