Journal: BioMed Research International

Article Title: MicroRNAs as Salivary Markers for Periodontal Diseases: A New Diagnostic Approach?

doi: 10.1155/2016/1027525

Figure Lengend Snippet: Comparison of methods from current investigations regarding miRNAs in periodontal disease.

Article Snippet: Naqvi et al. 2014 [ ] , Human THP-1-differentiated macrophages , miRNeasy kit (Qiagen) , NanoString nCounter miRNA assay (NanoString Technologies) , Quantitative real-time PCR EvaGreen Master Mix (Biotium) , — , RNU6B , Student's t -test (two-tailed) , miR-29b miR-32 miR-146a miR-891.

Techniques: Comparison, RNA Extraction, Biomarker Discovery, Control, In Vitro, Microarray, Isolation, TaqMan microRNA Assay, SYBR Green Assay, Labeling, Real-time Polymerase Chain Reaction, Virus, Quantitative RT-PCR, In Vivo, Expressing, Mann-Whitney U-Test

Journal: Genes and Immunity

Article Title: Transcriptome characterization of immune suppression from battlefield-like stress

doi: 10.1038/gene.2012.49

Figure Lengend Snippet: Comparison of transcript levels determined by two different assays and comparison of transcript levels with plasma protein levels. ( a ) Correlation of real-time QPCR and cDNA microarray data: real-time PCR reactions for each gene were carried out with three or more replicates. Trizol RNA isolation and cDNA microarrays were used. Significance levels: *0.001⩽ q <0.05, **1.0E-5⩽ q <0.001, *** q <1.0E-5— q stands for P -values after FDR correction. ( b ) Plasma protein concentrations (ELISA) compared with transcript levels (oligo and cDNA microarray): plasma concentrations of PRL, IGF1 and IGF2, TNFα and enzymatic activity of superoxide dismutase 1 (SOD1) assays were performed in triplicate on the plasma of 9 of the 10 soldiers who completed RASP. The IGF-I depletion is consistent with the finding of other investigators who measured its plasma concentration on similar subjects (*0.01⩽ P <0.05, **0.001⩽ P <0.01, *** P <0.001).

Article Snippet: Expression profiles of miRs were assayed using Agilent's human miRNA v3 microarrays (Agilent Technologies Inc.) consisting of 15k targets representing 961 miRs.

Techniques: Microarray, Real-time Polymerase Chain Reaction, Isolation, Enzyme-linked Immunosorbent Assay, Activity Assay, Concentration Assay

Journal: Genes and Immunity

Article Title: Transcriptome characterization of immune suppression from battlefield-like stress

doi: 10.1038/gene.2012.49

Figure Lengend Snippet: Expression of immune response genes in leukocytes exposed ex vivo to SEB. Leukocytes isolated from whole blood were treated with SEB (∼10 6 cells ml −1 in RPMI 1640 and 10% human AB serum at a final concentration of 100 ng ml −1 SEB). Total RNA was isolated using Trizol and expression levels were profiled using cDNA microarrays. Shown here are the 151 RASP-suppressed immune response genes that passed Welch's test and FDR correction ( q <0.05). ( a ) Lanes left to right: pre-RASP samples not exposed to SEB (control), pre-RASP samples exposed to SEB, post-RASP samples not treated with SEB, post-RASP samples exposed to SEB. For comparative visualization purpose, expression values of the other groups were transformed against the pre-RASP control samples (black lane). Heat map of the same data without transformation is given in the supplement . ( b ) Expression values in SEB exposed leukocytes (in both the pre- and post-RASP conditions) were compared with the corresponding SEB untreated groups (pre-RASP control and post-RASP stressed groups). ( c ) Heat map of the 151 immune response genes in SEB treated groups (in both pre- and post-RASP leukocytes) clustered after subtraction of the corresponding baseline responses (cluster after subtraction of their expressions in the corresponding untreated groups shown in Figure 4b). clearly shows poor response of post-RASP leukocytes towards SEB exposure compared with pre-RASP leukocytes.

Article Snippet: Expression profiles of miRs were assayed using Agilent's human miRNA v3 microarrays (Agilent Technologies Inc.) consisting of 15k targets representing 961 miRs.

Techniques: Expressing, Ex Vivo, Isolation, Concentration Assay, Transformation Assay

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