Journal: Cell Death & Disease

Article Title: MiR-210-3p protects endometriotic cells from oxidative stress-induced cell cycle arrest by targeting BARD1

doi: 10.1038/s41419-019-1395-6

Figure Lengend Snippet: a Differentially expressed miRNAs between normoxia and hypoxia pre-treated primary cultured endometrial stromal cells (ESCs) ( n = 2) were determined by high-throughput sequencing and presented by the heat map. Each column represents one library, and the colour bar indicates relative expression level from high (red) to low (green). Red represents miRNAs showing a >2-fold change of expression; black represents miRNAs showing 1/2 < fold change ≤ 2; and green represents miRNAs showing a fold change ≤1/2. Hierarchical cluster analysis indicated that expression of miR-210-3p was high both in normoxia- and hypoxia-treated cells and was significantly upregulated after hypoxic treatment for 48 h. b Quantitative reverse transcriptase PCR (qRT-PCR) assay of miR-210-3p and HIF-1α mRNA expression in ESCs and Ishikawa cells cultured under normoxia or hypoxia. The bars show the mean value of three independent experiments ± standard deviation ( n = 5 for ESCs). * P < 0.05 vs. normoxia, paired Student t- test. c qRT-PCR assay of miR-210-3p expression in human normal endometrium, paired eutopic endometrium and ectopic lesions ( n = 15). * P < 0.05 vs. normal endometria, Mann–Whitney U test. d Fluorescence in situ hybridisation analyses using an oligonucleotide probe complementary to miR-210-3p on 5 μm sections of eutopic, ectopic endometrium and normal control tissues ( n = 5). Scale bars = 50 μm. Original magnification: ×400. Blue represents DAPI; green represents miR-210-3p signal. e Representative immunofluorescence double staining images of ectopic lesion with anti-CD10 and anti-Pan-cytokeratin (Pan-CK) antibody. CD10, a stromal cell marker (green); Pan-CK, a glandular cell marker (red); DAPI staining for nuclei (blue). Scale bars = 50 μm. Original magnification: ×400. f Percentages of cells in G1, S and G2/M phases in ESCs and Ishikawa with (LV-In-210) or without (LV-In-CN) miR-210-3p knockdown cultured under normoxia or hypoxia conditions. The bars show the mean percentages of three independent experiments ± standard deviation ( n = 5 for ESCs). * P < 0.05 vs. LV-In-210 under normoxia, # P < 0.05 vs. LV-In-CN under hypoxia, one-way ANOVA with LSD for multiple comparisons. g Western blot of cell cycle activators Cdc2 and cyclin B1 and inhibitors p53 and p21 in ESCs (left panel) and Ishikawa cells (right panel) infected with LV-In-CN or LV-In-210 under normoxia or hypoxia ( n = 5 for ESCs)

Article Snippet: ESCs were collected after hypoxic or normoxic culture for 48 h and then sent to RiboBio (RiboBio Co. Ltd, Guangzhou, China) for miRNA high-throughput sequencing analysis.

Techniques: Cell Culture, Next-Generation Sequencing, Expressing, Quantitative RT-PCR, Standard Deviation, MANN-WHITNEY, Fluorescence, In Situ, Hybridization, Immunofluorescence, Double Staining, Marker, Staining, Western Blot, Infection

Journal: Bioactive Materials

Article Title: Dual-engineered cartilage-targeting extracellular vesicles derived from mesenchymal stem cells enhance osteoarthritis treatment via miR-223/NLRP3/pyroptosis axis: Toward a precision therapy

doi: 10.1016/j.bioactmat.2023.06.012

Figure Lengend Snippet: miR-223 mediates the inhibitory effect of hUC-EVs on NLRP3 (A) Volcano plot illustrating miR expression of OA rat knee joint cartilage treated with or without hUC-EVs. Red dots, up-regulated miRs, blue dots, down-regulated miRs, gray dots, miRs with no significant difference. (B) Heat map of miRNA sequencing (miRNA-seq) analysis. Red arrow: miR-223. (Red: high expression, blue: low expression, n = 3 per group) (C) qRT-PCR analysis of miR-223 (n = 3 per group). (D) Binding seq of NLRP3 and miR-223. (E) Dual-luciferase reporter gene assay validating the interaction between NLRP3 and miR-223. (F) Protein levels of NLRP3 examined by western blotting. **P < 0.01. These experiments were repeated three times independently, and representative results are shown.

Article Snippet: To further investigate the underlying mechanism of hUC-EVs promoting chondrocyte survival and cartilage repair, we performed high-throughput miRNA sequencing (service provided by BGI, Shenzhen) of cartilage tissues in the PBS group and hUC-EVs group.

Techniques: Expressing, Sequencing, Quantitative RT-PCR, Binding Assay, Luciferase, Reporter Gene Assay, Western Blot

Journal: Oncotarget

Article Title: By inhibiting snail signaling and miR-23a-3p, osthole suppresses the EMT-mediated metastatic ability in prostate cancer

doi:

Figure Lengend Snippet: A. A schematic representation of the procedure for miRNA selection. Differential expressions of miRNAs in osthole-treated cells versus vehicle-treated cells were analyzed with a OneArray ® miRNA profiling chip. B. Treatment of Du145 cells with osthole for 6 h. miR-146a, miR-22-3p, and miR-23a-3p expressions were detected by a quantitative PCR. C. Upper panel, Du145 cells were transfected with an miR-23a-3p mimic or mimic control for 24 h followed by osthole (60 μM) treatment for an additional 24 h. E-cadherin expression levels were determined by a Western blot analysis. Quantitative E-cadherin protein levels were adjusted to the β-actin protein level. Lower panel, Relative luciferase activities of DU145 cells co-transfected with an E-cadherin luciferase 3′UTR reporter vector and miR-23a-3p mimic or mimic control for 24 h. Values are presented as the mean ± SE of three independent experiments. * p < 0.05, compared to the control groups. D. DU145 cells were transfected with an miR-23a-3p mimic or mimic control for 24 h followed by osthole (60 μM) treatment for an additional 24 h. The cell-invasion ability was determined by a Matrigel invasion assay. Values are presented as the mean ± SE of three independent experiments. Data were analyzed using a one-way ANOVA with Tukey's post-hoc tests at 95% confidence intervals; different letters represent different levels of significance. E. DU145 cells were transfected with either an miR-23a-3p inhibitor or a negative control. The cell-invasion ability was determined by a Matrigel invasion assay. Values are presented as the mean ± SE of three independent experiments. * p < 0.05, compared to the control groups. F. PC3 or DU145 cells were treated with TGF-β for 6, 12, or 24 h. Expression levels of E-cadherin and miR-23a-3p were determined by Western blotting (upper panel) and a quantitative PCR (lower panel), respectively. Quantitative E-cadherin protein levels were adjusted to the β-actin protein level.

Article Snippet: To identify which miRNAs are regulated by osthole, a high-throughput and specific miRNA microarray (human miRNA OneArray ® miRNA profiling chip) using Du145 cells after osthole treatment was conducted by the Phalanx Biotech Group (Hsinchu, Taiwan).

Techniques: Selection, Real-time Polymerase Chain Reaction, Transfection, Expressing, Western Blot, Luciferase, Plasmid Preparation, Invasion Assay, Negative Control

Journal: Frontiers in Plant Science

Article Title: Arabidopsis microRNA expression regulation in a wide range of abiotic stress responses

doi: 10.3389/fpls.2015.00410

Figure Lengend Snippet: Differential expression of Arabidopsis thaliana pri-miRNAs (white background) and mature miRNAs (gray background) under different abiotic stress conditions . Blue, red, and green colors indicate pri-miRNAs and mature miRNAs unchanged, upregulated and downregulated, respectively. (A) Upper panel depicts 30%SWC and 20%SWC drought stress (D30 and D20, respectively), middle panel shows half an hour and 6 h heat stress (H 0.5; H 6), lower panel shows 250 mM salinity (NaCl+), (B) upper panel presents copper deficiency (Cu−) and 10 μM copper excess (Cu+), lower panel depicts 10 μM cadmium excess (Cd+) and sulfur deficiency (S−). The fold change-based numbers of up- and downregulated pri-miRNAs and mature miRNAs shown in Venn diagrams were suggested by a two-tailed Student t test ( p ≤ 0.05) for pri-miRNA RT-qPCR analyses (modified mirEX high throughput real-time PCR platform, Bielewicz et al., , http://comgen.pl/mirex2/ ) and a One-Way Anova test ( p ≤ 0.05) for mature miRNA analyses by small RNA NGS, respectively.

Article Snippet: The abundance of the selected microRNAs was tested using Northern hybridization (for detailed data see Tables S2, S3 and Figures , ) as well as TaqMan® miRNA assays (ABI, Life Technologies, USA) (Figure S2).

Techniques: Quantitative Proteomics, Two Tailed Test, miRNA RT, Modification, High Throughput Screening Assay, Real-time Polymerase Chain Reaction

Journal: Frontiers in Plant Science

Article Title: Arabidopsis microRNA expression regulation in a wide range of abiotic stress responses

doi: 10.3389/fpls.2015.00410

Figure Lengend Snippet: Arabidopsis thaliana miRNAs revealed by Northern hybridization as affected under 30%SWC mild drought, 20%SWC severe drought, 0.5 h heat, 6 h heat, and salinity stress conditions . Only new stress responsive miRNAs unknown until now are shown. The white lines separate signals from miRNAs and U6snRNA loading control probed on the same blots. H 0 and H 6 samples were run on the same gel but not next to each other as indicated by the white separating lines between all signals probed. The star marks NGS revealed miRNAs with no statistic significance and the maintained tendency of expression level change as seen in Northern hybridization. Symbols representing various stresses are marked as described in the Figure .

Article Snippet: The abundance of the selected microRNAs was tested using Northern hybridization (for detailed data see Tables S2, S3 and Figures , ) as well as TaqMan® miRNA assays (ABI, Life Technologies, USA) (Figure S2).

Techniques: Northern Blot, Hybridization, Control, Expressing

Journal: Frontiers in Plant Science

Article Title: Arabidopsis microRNA expression regulation in a wide range of abiotic stress responses

doi: 10.3389/fpls.2015.00410

Figure Lengend Snippet: Arabidopsis thaliana miRNAs revealed by Northern hybridization as affected under copper deficiency, copper excess, cadmium excess, and sulfur deficiency stress conditions . Only new stress responsive miRNAs unknown until now are shown. The white lines separate signals from miRNAs and U6snRNA loading control probed on the same blots. Control (Ctrl) and stress (Cu−, Cu+, Cd+, S−) samples were run on the same gel but not next to each other as indicated by the white separating lines between all signals probed. The star marks NGS revealed miRNAs with no statistic significance and the maintained tendency of expression level change as seen in Northern hybridization. Symbols representing various stresses are marked as described in the Figure .

Article Snippet: The abundance of the selected microRNAs was tested using Northern hybridization (for detailed data see Tables S2, S3 and Figures , ) as well as TaqMan® miRNA assays (ABI, Life Technologies, USA) (Figure S2).

Techniques: Northern Blot, Hybridization, Control, Expressing

Journal: Frontiers in Plant Science

Article Title: Arabidopsis microRNA expression regulation in a wide range of abiotic stress responses

doi: 10.3389/fpls.2015.00410

Figure Lengend Snippet: Individual pri-miRNA—miRNA relationships under different abiotic stresses .

Article Snippet: The abundance of the selected microRNAs was tested using Northern hybridization (for detailed data see Tables S2, S3 and Figures , ) as well as TaqMan® miRNA assays (ABI, Life Technologies, USA) (Figure S2).

Techniques:

Journal: Frontiers in Plant Science

Article Title: Arabidopsis microRNA expression regulation in a wide range of abiotic stress responses

doi: 10.3389/fpls.2015.00410

Figure Lengend Snippet: 30%SWC (D30) and 20%SWC (D20) drought stress affected Arabidopsis miRNAs revealed by high-throughput small RNA NGS .

Article Snippet: The abundance of the selected microRNAs was tested using Northern hybridization (for detailed data see Tables S2, S3 and Figures , ) as well as TaqMan® miRNA assays (ABI, Life Technologies, USA) (Figure S2).

Techniques:

Journal: Frontiers in Plant Science

Article Title: Arabidopsis microRNA expression regulation in a wide range of abiotic stress responses

doi: 10.3389/fpls.2015.00410

Figure Lengend Snippet: 0.5 h (H 0.5) and 6 h (H 6) heat stress affected Arabidopsis miRNAs revealed by high-throughput small RNA NGS .

Article Snippet: The abundance of the selected microRNAs was tested using Northern hybridization (for detailed data see Tables S2, S3 and Figures , ) as well as TaqMan® miRNA assays (ABI, Life Technologies, USA) (Figure S2).

Techniques:

Journal: Frontiers in Plant Science

Article Title: Arabidopsis microRNA expression regulation in a wide range of abiotic stress responses

doi: 10.3389/fpls.2015.00410

Figure Lengend Snippet: Salinity (NaCl+) stress affected Arabidopsis miRNAs revealed by high-throughput small RNA NGS .

Article Snippet: The abundance of the selected microRNAs was tested using Northern hybridization (for detailed data see Tables S2, S3 and Figures , ) as well as TaqMan® miRNA assays (ABI, Life Technologies, USA) (Figure S2).

Techniques:

Journal: Frontiers in Plant Science

Article Title: Arabidopsis microRNA expression regulation in a wide range of abiotic stress responses

doi: 10.3389/fpls.2015.00410

Figure Lengend Snippet: Copper deficiency (Cu−), copper excess (Cu+), cadmium excess (Cd+), and sulfur deficiency (S−) stresses affected Arabidopsis miRNAs revealed by high-throughput small RNA NGS .

Article Snippet: The abundance of the selected microRNAs was tested using Northern hybridization (for detailed data see Tables S2, S3 and Figures , ) as well as TaqMan® miRNA assays (ABI, Life Technologies, USA) (Figure S2).

Techniques:

Journal: Frontiers in Plant Science

Article Title: Arabidopsis microRNA expression regulation in a wide range of abiotic stress responses

doi: 10.3389/fpls.2015.00410

Figure Lengend Snippet: General stress-responsive miRNAs . (A) General abiotic stress responsive Arabidopsis thaliana miRNAs 319a/b, 319b.2, and 400 revealed by Northern hybridization under different abiotic stresses. The white lines separate signals from miRNAs and U6snRNA loading control as well as both signals for the following stress samples: NaCl+ and Cu− (for miR319a/b), control (Ctrl) and Cu− (for miR319b.2), Cd+ and H 0 (for miR400), all probed on the same blots. (B) The structure of the TBL10 and the predicted as well as 5′RACE identified slicing sites within its mRNAs. (C) The agarose gels showing the miR319b.2 directed 3′-TBL10 mRNA cleavage products in wt plants and Δ miR319b mutant plants. Arrow points to the expected length of the 5′RACE product. (D) The RT-qPCR of the TBL10 expression in wt plants under different abiotic stress conditions. Values on the chart are shown as the mean ± SD relative expression level from three independent experiments. Symbols representing various stresses are marked as described in the Figure .

Article Snippet: The abundance of the selected microRNAs was tested using Northern hybridization (for detailed data see Tables S2, S3 and Figures , ) as well as TaqMan® miRNA assays (ABI, Life Technologies, USA) (Figure S2).

Techniques: Northern Blot, Hybridization, Control, Mutagenesis, Quantitative RT-PCR, Expressing

Journal: Frontiers in Plant Science

Article Title: Arabidopsis microRNA expression regulation in a wide range of abiotic stress responses

doi: 10.3389/fpls.2015.00410

Figure Lengend Snippet: General stress-responsive Arabidopsis microRNAs revealed by high-throughput small RNA NGS .

Article Snippet: The abundance of the selected microRNAs was tested using Northern hybridization (for detailed data see Tables S2, S3 and Figures , ) as well as TaqMan® miRNA assays (ABI, Life Technologies, USA) (Figure S2).

Techniques:

Journal: Clinical Science (London, England : 1979)

Article Title: Osteoclast-derived exosomal miR-30a-3p promotes lead exposure-induced osteoporosis by triggering osteoblastic pyroptosis

doi: 10.1042/CS20243438

Figure Lengend Snippet: (A ) Schematic diagram of the sequencing design of plasma-Exos and OC-Exos. Plasma-Exos from Pb-exposed low-BMD (group A), Pb-exposed normal BMD (group B), low BMD (group C), and healthy control (group D) groups and 5-μM PbAc OC-Exos were collected for sequencing. ( B ) Heatmap of differentially expressed plasma-Exo-miRNAs in groups A and B. Red and green indicate high expression levels and low expression levels, respectively. ( C ) Heatmap of differentially expressed plasma-Exo-miRNAs in groups A and C. Red and green indicate high expression levels and low expression levels, respectively. ( D ) Partial heatmap of differentially expressed plasma-Exo-miRNAs in groups A and D. Red and green indicate high expression levels and low expression levels, respectively. ( E ) Volcano plots of plasma-Exo-miRNAs in groups A and B. The red and green plots indicate the differentially expressed plasma-Exo-miRNAs. ( F ) Volcano plots of plasma-Exo-miRNAs in groups A and C. The red and green plots indicate the differentially expressed plasma-Exo-miRNAs. ( G ) Volcano plots of plasma-Exo-miRNAs in groups A and D. The red and green plots indicate the differentially expressed plasma-Exo-miRNAs. ( H ) Partial heatmap of differentially expressed OC-Exo-miRNAs in 5 μM PbAc and control. Red and green indicate high expression levels and low expression levels, respectively. ( I ) Venn diagram showing the overlapping numbers of differentially expressed miRNAs in the plasma-Exos and OC-Exos. ( J ) Real-time PCR analysis of the differential expression of miR-30a-3p in plasma-Exos between Pb-exposed low-BMD, Pb-exposed normal-BMD, and healthy control groups. U6 small nuclear RNA was used as the internal control. ( K ) ROC curve was used to analyze the diagnostic ability of miR-30a-3p in Pb-induced osteoporosis patients. The true-positive rate and the false-positive rate of ROC curve were calculated using the true-positive rate and the false-positive rate as the horizontal and vertical co-ordinates, respectively. BMD, bone mineral density; OCs, osteoclasts; PbAc, lead acetate.

Article Snippet: The miRNA high-throughput sequencing was performed by CloudSeq Biotech (Shanghai, China).

Techniques: Sequencing, Clinical Proteomics, Control, Expressing, Real-time Polymerase Chain Reaction, Quantitative Proteomics, Diagnostic Assay

Journal: iScience

Article Title: Screening and molecular mechanism research on bile microRNAs associated with chemotherapy efficacy in perihilar cholangiocarcinoma

doi: 10.1016/j.isci.2024.111437

Figure Lengend Snippet: High-throughput sequencing results (A–C) Sequencing and qPCR validation of bile miRNAs. (D) Sequencing of bile mRNAs. (E and F) KEGG pathway analysis of the upregulated mRNAs in the bile of patients with dismal prognosis (E) and better prognosis (F). Data are represented as mean ± SD. n = 4, ∗ p < 0.05, ∗∗ p < 0.01, ∗∗∗ p < 0.001, ns: no significance, miRNAs microRNAs, qPCR quantitative polymerase chain reaction, KEGG Kyoto Encyclopedia of Genes and Genomes.

Article Snippet: High-throughput sequencing of miRNAs and mRNAs , CloudSeq Biotech Inc , N/A.

Techniques: Next-Generation Sequencing, Sequencing, Real-time Polymerase Chain Reaction

Journal: iScience

Article Title: Screening and molecular mechanism research on bile microRNAs associated with chemotherapy efficacy in perihilar cholangiocarcinoma

doi: 10.1016/j.isci.2024.111437

Figure Lengend Snippet:

Article Snippet: High-throughput sequencing of miRNAs and mRNAs , CloudSeq Biotech Inc , N/A.

Techniques: Virus, Recombinant, Next-Generation Sequencing, Reverse Transcription, Bicinchoninic Acid Protein Assay, Western Blot, Control, Plasmid Preparation, Software

Journal: PLoS ONE

Article Title: Identification of novel biomarkers to monitor β-cell function and enable early detection of type 2 diabetes risk

doi: 10.1371/journal.pone.0182932

Figure Lengend Snippet: 11 miRNAs were identified as differentially expressed at both time-points; 6 miRNAs were predictive of ß-cell glucose sensitivity at baseline only; and 16 only at follow-up.

Article Snippet: RT-PCR based miRNA high-throughput detection according to Regulus Therapeutics’ proprietary method was used ( http://regulusrx.com/ ) to measure 754 micro-RNAs.

Techniques: