Journal: Gene

Article Title: Comparative profiling of miRNA expression of lung adenocarcinoma cells in two-dimensional and three-dimensional cultures

doi: 10.1016/j.gene.2012.09.093

Figure Lengend Snippet: Distinct miRNA profiles of mK-ras-LE cells in 2-D and rBM 3-D cultures. A) mK-ras-LE cells were grown in 2-D and rBM 3-D culture. Morphology of the cells was visualized using fluorescent staining for F-actin. The images of rBM 3-D culture were captured at the central planes of cell clusters using a confocal fluorescent microscope on day 12 post-seeding. The images were captured at 600x magnification. Representative images of each culture condition were displayed. B) Total cell RNA was extracted from mK-ras-LE cells in 2-D and rBM 3-D cultures. miRNA expression profiles were compared between the two culture conditions using miRNA microarrays. A heatmap of the significantly differentially expressed miRNAs was generated using geWorkbench suite (n = 3, P < 0.01, FDR < 0.05). C) The expression of miR-17, miR-92b, and miR-21 was measured using qRT-PCR in total cell RNA collected from 2-D and rBM 3-D cultures of mK-ras-LE cells. A fold change of each miRNA of interest was obtained by setting the values of each miRNA in 2-D culture to one and normalization to the values of U6. D) Similar to part C except that the expression of miR-200a was compared between 2-D and rBM 3-D cultures. E) The culture conditions were similar to part A. The cell lysates were collected from the cell colonies extracted from the culture. The protein levels of ZEB2, PTEN, and -actin were determined using immunoblots. The data were presented in averages and standard deviations obtained from three independent experiments. and indicated a P value < 0.05 and 0.01, respectively.

Article Snippet: 2.4. miRNA microarray analysis The miRNA expression profiling service was provided by LC Sciences (Houston, TX) using μParaflo® technology and proprietary probe hybridization (Cy3 and Cy5 dendrimer dyes) that enables highly sensitive and specific direct detection of mouse miRNAs.

Techniques: Staining, Microscopy, Expressing, Generated, Quantitative RT-PCR, Western Blot

Journal: Gene

Article Title: Comparative profiling of miRNA expression of lung adenocarcinoma cells in two-dimensional and three-dimensional cultures

doi: 10.1016/j.gene.2012.09.093

Figure Lengend Snippet: Disparate expression of miRNAs between rBM 3-D and 2-D cultures of mK-ras-LE cells. Total cell RNA was extracted from rBM 3-D and 2-D cultures. miRNA arrays were carried out and analyzed as described in Methods. A fold change of each miRNA was obtained by setting the values from 2-D culture to one. The results were average of three miRNA microarrays. The miRNAs bearing documented tumor-modulating properties were highlighted in bold.

Article Snippet: 2.4. miRNA microarray analysis The miRNA expression profiling service was provided by LC Sciences (Houston, TX) using μParaflo® technology and proprietary probe hybridization (Cy3 and Cy5 dendrimer dyes) that enables highly sensitive and specific direct detection of mouse miRNAs.

Techniques: Expressing

Journal: Gene

Article Title: Comparative profiling of miRNA expression of lung adenocarcinoma cells in two-dimensional and three-dimensional cultures

doi: 10.1016/j.gene.2012.09.093

Figure Lengend Snippet: miRNA expression associated with aincar morphogenesis. A) A549 and A549LC cells were cultured in 2-D (A1 & A2) and rBM 3-D (A3 & A4) cultures. Morphology was recorded using an inverse phase contrast microscope. Polarized monolayer of the cells and the central lumen were pointed at by white arrows. B) The expression of miR-17, miR-92, and miR-21 was measured using qRT-PCR in total cell RNA collected from 2-D and rBM 3-D of A549 and A549LC cells. A fold change of each miRNA was obtained by setting the values of each miRNA from A549 cells in 2-D culture to one and normalization to the values of U6. C) Similar to part A except that the expression of miR-200a was compared across the groups. D) The culture conditions were similar to part A. The RNA levels of pri-miR-21 and VMP1 were measured in A549 cells using qRT-PCR. A fold change of each RNA was obtained by setting the values of RNA from A549 cells in 2-D culture to one and normalization to the values of 36B4. The data were presented in averages and standard deviations obtained from three independent experiments. , , and indicated a P value < 0.05, 0.01, and 0.001, respectively.

Article Snippet: 2.4. miRNA microarray analysis The miRNA expression profiling service was provided by LC Sciences (Houston, TX) using μParaflo® technology and proprietary probe hybridization (Cy3 and Cy5 dendrimer dyes) that enables highly sensitive and specific direct detection of mouse miRNAs.

Techniques: Expressing, Cell Culture, Microscopy, Quantitative RT-PCR

Journal: Circulation Research

Article Title: Inhibition of miR-15 Protects Against Cardiac Ischemic Injury

doi: 10.1161/CIRCRESAHA.111.244442

Figure Lengend Snippet: A, Representative images after TTC staining indicate that although the area at risk (AAR, red and white) is comparable between the different treatment groups, the infarcted area (IA, white) is smaller in the tiny 15b-treated animals (control indicates control oligonucleotide). B, Quantification of cross sections of the infarcted hearts indicate that the AAR is ≈50% of the LV for all 3 treatment groups, whereas administration of 0.5 mg/kg of tiny 15b during reperfusion results in a significant reduction in infarct size compared with either saline or control oligo (*P<0.05 versus saline and control by ANOVA; control indicates control oligonucleotide). C, Real-time PCR analysis on tissue of the ischemic region 24 hours after reperfusion indicates inhibition of miR-15b in response to tiny 15b treatment (*P<0.05 versus saline and control oligonucleotide treated by ANOVA). D, Left ventricular end-diastolic pressure recordings 24 hours after reperfusion reveals an increase with saline treatment and a reduction with tiny 15b treatment (control indicates control oligonucleotide, *P<0.05 versus sham Kruskal-Wallis test). E, Ontology analysis of transcripts upregulated ≥1.5-fold in the ischemic region of hearts 24 hours after reperfusion treated with tiny 15b treatment compared with saline, based on microarray profiling. Negative regulators of apoptosis and cell death are significantly overrepresented. F, Echocardiography shows a reduction in ejection fraction (EF) and increases in LV volumes 2 weeks after infarct, all of which are significantly improved in response to tiny 15b treatment (*P<0.05 versus saline and control by ANOVA for EF and LVESV, versus saline only LVEDV; sham indicates no ischemia/reperfusion; control, control oligo). G, Representative images of Picrosirius red-stained cross sections demonstrate a reduction in collagen content of the left ventricle 2 weeks after reperfusion with tiny 15b treatment. Quantification of fibrosis as a percentage of total left ventricular area reveals a statistically significant reduction in the tiny 15b-treated group (*P<0.05 versus saline-treated by ANOVA). LV indicates left ventricle.

Article Snippet: Microarray for miRNAs and mRNAs Microarray analysis was performed on total RNA, using a service provider (LC Sciences, Houston, TX) as described previously.

Techniques: Staining, Control, Saline, Real-time Polymerase Chain Reaction, Inhibition, Microarray

Journal: Annals of Medicine

Article Title: MiR-223-3p regulates erythropoiesis by targeting TGFBR3/Smad signaling pathway in hemoglobin H-Constant Spring disease

doi: 10.1080/07853890.2025.2530690

Figure Lengend Snippet: Comparison of the expression profiles of miRNAs(A-C) and mRNAs (D-F) between HbH-CS patients and healthy controls. (A) Scatter plot showing the distribution of miRNA expression. (B) Volcano plot showing the differential expression of miRNAs. (C) The clustering heatmap showed differentially expressed miRNAs between patients with HbH-CS patients and healthy controls. (D) Scatter plot showing the distribution of mRNA expression. (E) Volcano plot showing the differential expression of mRNAs. (F) The clustering heatmap showed differentially expressed mRNAs between patients with HbH-CS patients and healthy controls.

Article Snippet: MiRNAs associated with hematopoietic cell lineage, apoptosis, and cell cycle were searched in the database, which were stratified by Arraystar miRNA expression profiling microarray data filtered according to p < 0.05 and log FC >1.5.

Techniques: Comparison, Expressing, Quantitative Proteomics

Journal: Annals of Medicine

Article Title: MiR-223-3p regulates erythropoiesis by targeting TGFBR3/Smad signaling pathway in hemoglobin H-Constant Spring disease

doi: 10.1080/07853890.2025.2530690

Figure Lengend Snippet: Bioinformatics analysis. (A) Venn diagram showed stratified operations of miRNAs from the original data and online database. (B) Intersection plot of mRNAs from our previous ArrayStar human mRNA array and miR-223-3p target gene predicted by online database. (C) Prediction plot of miR-223-3p target gene. Yellow circled node, miR-223-3p; blue rectangle type node, mRNA. (D, E) The qRT-PCR was performed to detect the relative expression levels of miR-223-3p (D) and TGFBR3 (E) in the samples from healthy normal subjects and HbH-CS patients. Normal group, n = 17; HbH-CS group, n = 17, mean ± SEM, ** p < 0.01, *** p < 0.001.

Article Snippet: MiRNAs associated with hematopoietic cell lineage, apoptosis, and cell cycle were searched in the database, which were stratified by Arraystar miRNA expression profiling microarray data filtered according to p < 0.05 and log FC >1.5.

Techniques: Quantitative RT-PCR, Expressing

Journal: The FASEB Journal

Article Title: Extracellular vesicles extracted from young donor serum attenuate inflammaging via partially rejuvenating aged T-cell immunotolerance

doi: 10.1096/fj.201800059R

Figure Lengend Snippet: Characteristics of serum-extracted EVs. A) Comparison of the sizes of EVs extracted from young murine serum by the ExoQuick reagent pretreated with and without using 0.2-μm filters. B) Morphology of EVs from young murine serum used in this project for rejuvenation of inflammaging, photographed by atomic force microscopy (AFM). C, D) Different miRNA expression profiles in heatmap (C) and quantified summary (D) of EVs from young vs. old murine serum, analyzed by murine miRNA microarray with Mus musculus miRBase version-21 arrays that contained 1900 unique mature miRNA probes (miRNA microarray service via LC Sciences).

Article Snippet: Then, 1–3 μg of total RNAs for each sample were used for customized miRNA microarray service from LC Sciences (Houston, TX, USA).

Techniques: Comparison, Microscopy, Expressing, Microarray