microarray hybridisation and data normalisation analyses  (CapitalBio Corporation)

Journal: Respiratory Research

Article Title: Exosomal microRNAs of tuberculous pleural effusion orchestrating TGF-β signaling mediate pleural fibrosis

doi: 10.1186/s12931-026-03541-5

Figure Lengend Snippet: Differentially expressed miRNA in exosomes from tuberculous pleural effusion and transudative pleural effusion (as control) by miRNAs sequencing. A Heatmap of differential exosomes miRNAs expression in pleural effusion between control individuals and tuberculous pleurisy patients; n = 9. RPKM values are represented by gradient colors and shown for each sample. Red represents a higher RPKM; blue represents a lower RPKM. Results are based on nine RNA sequencing samples. B Venn diagram showing the overlap between differentially expressed miRNAs in TPE exosomes and transudate exosomes. C Volcanic map of differential exosomes miRNAs expression in pleural effusion between control individuals and tuberculous pleurisy patients. Adjusted P value < 0.05 and fold change > 1 was set as restrictive conditions to identify the differentially expressed genes. D Pathway enrichment analysis showed the significant target genes of differentially expressed miRNAs associated with various KEGG pathways. E The expression of three differentially expressed miRNAs in TPE exosomes and transudate exosomes was verified by RT-qPCR and normalized by the U6. Data are expressed as mean ± SEM. n = 6, **** P < 0.0001 (Paired student’s t-test)

Article Snippet: Exosomes from pleural effusion were obtained by ultracentrifugation of samples isolated from nine control individuals and nine patients with tuberculous pleurisy patients and processed by Novogene Co., Ltd (Beijing, China) for miRNA microarray analysis (lllumina SE50).

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

Journal: Respiratory Research

Article Title: Exosomal microRNAs of tuberculous pleural effusion orchestrating TGF-β signaling mediate pleural fibrosis

doi: 10.1186/s12931-026-03541-5

Figure Lengend Snippet: miR-503-5p regulated Smurf1/Smad7 signaling pathway. A , B Venn diagram showing overlap between differentially up-regulated miRNAs in TPE exosomes and miRNAs targeting Smurf1 or Smad7 predicted by the miRTarBase. The online analysis database “miRTarBase” ( https://miRTarBase.cuhk.edu.cn/ ) was used. C Human PMCs were transfected with miR-503-5p mimics (50 nmol/ml) or negative control (NC) for 24 h, after which miR-503-5p expression levels in cells were determined by qRT-PCR and normalized by the U6. D - E Human PMCs were transfected with miR-25-3p mimics or miR-503-5p mimics or miR-92a-3p mimics (50 nmol/ml) or negative control (NC) for 24 h, after which intracellular mRNA levels of Smurf1 were measured by RT-qPCR and normalized to GAPDH ( D ). The protein expression of Smurf1 and TGF-β receptor (TGFBR) were detected by western blotting. Bar graphs revealed changes in relative ratio of Smurf1 and TGFBR to GAPDH. F Human PMCs were transfected with miR-503-5p mimics (50 nmol/ml) or negative control (NC) for 24 h, after which mRNA expression of Smurf1, TGFBR and COL1A1 were detected by qRT-PCR. G Human PMCs were incubated with miR-503-5p mimics. After 24 h, Smurf1 protein was detected by immunofluorescence staining and nuclei with DAPI staining. Bar scale: 50 μm. H - K Human PMCs were transfected with miR-503-5p mimics (50 nmol/ml) or negative control (NC) for 24 h. miR-503-5p expression levels in cells were determined by qRT-PCR and normalized by the U6 ( H ). The protein expression of S Smurf1, TGFBR and COL1A1 were detected by western blotting ( I ). Bar graphs revealed changes in the relative ratio to GAPDH ( J ). mRNA levels of S Smurf1, TGFBR and COL1A1 were measured by RT-qPCR and normalized to GAPDH ( K ). Data are mean ± SEM. n = 3. * P < 0.05 (student’s t-test)

Article Snippet: Exosomes from pleural effusion were obtained by ultracentrifugation of samples isolated from nine control individuals and nine patients with tuberculous pleurisy patients and processed by Novogene Co., Ltd (Beijing, China) for miRNA microarray analysis (lllumina SE50).

Techniques: Transfection, Negative Control, Expressing, Quantitative RT-PCR, Western Blot, Incubation, Immunofluorescence, Staining

Journal: Respiratory Research

Article Title: Exosomal microRNAs of tuberculous pleural effusion orchestrating TGF-β signaling mediate pleural fibrosis

doi: 10.1186/s12931-026-03541-5

Figure Lengend Snippet: Triple miRNAs inhibitor attenuated TPE-Exo induced pleural fibrosis. C57BL/6 mice were intra-pleural injected by using PBS (100 µl/mouse), TPE-Exo (100 µl/mouse), TPE-Exo plus control inhibitor, or TPE-Exo plus triple miRNAs inhibitor with carbon particles (0.1 mg/mouse) as descriptions in the Methods. TPE-Exo from 50 ml TPE was administered at days 1, 5, 9. In TPE-Exo plus triple miRNAs inhibitor group, TPE-Exo was co-incubated with triple miRNAs inhibitor which restrained expressions of miR-150-3p, miR-424-3p and miR-503-5p. All mice were euthanized at day 21, and tissues were taken for analysis. A Representative Masson’s trichrome staining images of visceral pleura from lung sections, parietal pleura from chest wall and diaphragm sections. Original magnification, ×400. B Changes in pleural thickness. C Changes in collagen percentages of visceral and parietal pleura. Data are expressed as mean ± SEM. n = 6 mice. *** P < 0.001 (One-way ANOVA followed by the Bonferroni’s test)

Article Snippet: Exosomes from pleural effusion were obtained by ultracentrifugation of samples isolated from nine control individuals and nine patients with tuberculous pleurisy patients and processed by Novogene Co., Ltd (Beijing, China) for miRNA microarray analysis (lllumina SE50).

Techniques: Injection, Control, Incubation, Staining

Journal: Nucleic Acids Research

Article Title: A transcriptomic and proteomic map of primary human cell types

doi: 10.1093/nar/gkaf1498

Figure Lengend Snippet: Cell type specific genes demonstrated at mRNA level. (A) Heat map of genes with cell type specific expression. (B) Heat map of selected genes with endothelial or epithelial cell type specific expression. (C) Immunohistochemistry staining of protein C1orf116 across human tissues showing its epithelial cell type specific expression. The panel shows a magnified view (20×) from tissue microarrays.

Article Snippet: The Human Protein Atlas (HPA) project provided a tissue-based map of the human proteome through transcriptomics and tissue microarray-based immunohistochemistry analysis [ , ].

Techniques: Expressing, Immunohistochemistry, Staining

Journal: Materials Today Bio

Article Title: Empowering chemotherapy-induced antitumor immunity by multi-targeted synergistic combination nanomedicine for triple-negative breast cancer

doi: 10.1016/j.mtbio.2025.102445

Figure Lengend Snippet: Kaplan-Meier overall survival analyses of low and high CD4, CD8A, CD8B, ADGRE1, and IL-6 expression in the tumors of TNBC patients based on DNA microarray data. CD4 low: n = 436; CD4 high: n = 430; CD8A low: n = 434; CD8A high: n = 432; CD8B low: n = 457; CD8B high: n = 409; ADGRE1 low: n = 140; ADGRE1 high: n = 34; IL6 low: n = 469; IL6 high: n = 463.

Article Snippet: The gene expression profiles are generated through standardized DNA microarray analysis procedures, which involve RNA extraction from tumor samples, reverse transcription to cDNA, hybridization to oligonucleotide microarray chips (e.g., Affymetrix U133A or U133 Plus 2.0), followed by fluorescence-based signal detection and normalization using algorithms such as RMA or MAS5 [ ].

Techniques: Expressing, Microarray