Journal: Experimental cell research

Article Title: Rapamycin-induced modulation of miRNA expression is associated with amelioration of HIV-associated nephropathy (HIVAN)

doi: 10.1016/j.yexcr.2013.04.011

Figure Lengend Snippet: Differential expression of miRNAs in kidneys of Tg26 and rapamycin-treated Tg26 mice. (A) Heatmap depicts triplicate microarray hybridizations, revealing a subset of miRNAs that are differentially expressed in rapamycin-treated Tg26 mice compared with Tg26 and control FVB/N mice. The color scale shown at the bottom: green denotes expression >40 and red denotes an expression <0. (B) The relative expression of miRNAs level is present in log2 transformation. Total 3 miRNAs were upregulated (right) and 16 miRNAs were downregulated (left) in rapamycin-treated Tg26 mice (P<0.05).

Article Snippet: MicroRNA expression analysis was performed by LC Sciences Microarray Service (Houston, TX).

Techniques: Expressing, Microarray, Transformation Assay

Journal: Frontiers in Molecular Neuroscience

Article Title: A comprehensive characterization of the nuclear microRNA repertoire of post-mitotic neurons

doi: 10.3389/fnmol.2013.00043

Figure Lengend Snippet: MiRNA profiling by microarray after nucleo-cytoplasmic fractionation of neurons. (A) qRT-PCR analysis of marker genes to validate the fractionation protocol. The fold enrichment (y-axis) of marker genes in the nucleus was calculated by the 2 −dCt [2 −(NUC Ct−CYT Ct) ] method. Bar plots show mean ± standard deviation ( SD ; n = 3). Statistical significance was determined using Student's t -test with Bonferroni correction ( * p < 0.05; ** p < 0.01). (B) Northern blot analysis of the nuclear marker U6 snRNA in nuclear and cytoplasmic fractions. Intensity of the signal was quantified using ImageJ. (C) Detection of nuclear (HDAC2, histone deacetylase 2) and cytoplasmic (beta-Actin) marker proteins in the subcellular fractions using Western blotting assay. Whole cell lysate was used as an input sample. (D) Comparison of different biological replicates from microarray experiments. Pearson's correlation coefficients between indicated samples are shown. Data on gray background represents correlation coefficients for biological replicates from the same cellular fraction. (E) Distribution of miRNA expression in the nucleus and the cytoplasm. Scatterplot of log 2 transformed signal intensity values for miRNAs from nuclear (x-axis) and cytoplasmic (y-axis) fractions (267). Dots above the diagonal indicate cytoplasmic enrichment, below, nuclear enrichment of the respective miRNAs.

Article Snippet: For miRNA profiling analysis, 14 μl of small RNA, obtained from each sample, were sent to microRNA Microarray Service provided by LC Sciences (Texas, USA).

Techniques: Microarray, Fractionation, Quantitative RT-PCR, Marker, Standard Deviation, Northern Blot, Histone Deacetylase Assay, Western Blot, Comparison, Expressing, Transformation Assay

Journal: Frontiers in Molecular Neuroscience

Article Title: A comprehensive characterization of the nuclear microRNA repertoire of post-mitotic neurons

doi: 10.3389/fnmol.2013.00043

Figure Lengend Snippet: Comparison of miRNA expression profiles obtained from miRNA microarrays and small RNA deep sequencing. (A) Venn diagram illustrating miRNAs detected by the two different methods. 220 miRNAs were detected by both methods. (B,C) Scatterplot of log 2 transformed signal intensity values (microarray, y-axis) and read counts (deep sequencing, x-axis) for miRNAs detected in the nuclear (B) or cytoplasmic (C) fractions.

Article Snippet: For miRNA profiling analysis, 14 μl of small RNA, obtained from each sample, were sent to microRNA Microarray Service provided by LC Sciences (Texas, USA).

Techniques: Comparison, Expressing, Sequencing, Transformation Assay, Microarray

Journal: Frontiers in Molecular Neuroscience

Article Title: A comprehensive characterization of the nuclear microRNA repertoire of post-mitotic neurons

doi: 10.3389/fnmol.2013.00043

Figure Lengend Snippet: Developmental stage and cell-type-specific expression of the nuclear-enriched miRNAs, miR-25 and miR-92a. (A) Relative expression (normalized to U6 snRNA) levels of miR-25 and miR-92a during in vitro development of primary cortical neurons was determined by qRT-PCR analysis. Bar plots show mean ± SD ( n = 2). Statistical significance was determined using Student's t -test with Bonferroni correction ( * , p < 0.05). (B) Developmental expression score (DES; log 2 (P3/E10) from (Yao et al., ); y-axis) comparison of 10 highest and lowest ranked miRNAs. Error bars represent standard deviation from the mean DES within each group. Statistical significance was determined using Student's t -test ( p = 0.028). (C) Expression of miR-25 and miR-92a in mixed cultures and neuronal-enriched cultures (FUDR-treated). The relative expression levels of indicated RNAs were obtained by the ddCt method. RNA levels in mixed cultures were arbitrarily set to 1. Bar plots show mean ± SD ( n = 3). SD for mixed culture condition was determined after normalization to an internal control RNA (U6 snRNA). Statistical significance was determined based on U6 snRNA normalized values using Student's t -test with Bonferroni correction ( ** p < 0.01). (D) Nuclear-enrichment of miRNA expression in mixed and neuron-enriched (FUDR-treated) cultures. The expression level of miRNAs was determined using qRT-PCR analysis with TaqMan microRNA assay. Bar plots show mean ± SD ( n = 2). Statistical significance was determined using Student's t -test with Bonferroni correction ( * p < 0.05; ** p < 0.01).

Article Snippet: For miRNA profiling analysis, 14 μl of small RNA, obtained from each sample, were sent to microRNA Microarray Service provided by LC Sciences (Texas, USA).

Techniques: Expressing, In Vitro, Quantitative RT-PCR, Comparison, Standard Deviation, Control, TaqMan microRNA Assay

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

Journal: Sensors (Basel, Switzerland)

Article Title: Absolute Quantitation of Serum Antibody Reactivity Using the Richards Growth Model for Antigen Microspot Titration

doi: 10.3390/s22103962

Figure Lengend Snippet: Simultaneous titration of antigen density and serum antibody. Steps of the technology, starting with microarray fabrication and measurement, through image analysis to curve fitting and visualization of results are shown. Serum dilution is indicated by red drops, antigen density differences are represented by shades of blue circles. Several binding curves are transformed into one by fitting data with generalized logistic curves, yielding two parameters, x i and d, which characterize thermodynamic activity distribution of serum antibodies. Affinity is related to x i , the point of inflection; antibody heterogeneity is related to d, the asymmetry parameter. The slope at infinity “s” of the curve in the lower left corner is given by the equation shown.

Article Snippet: K.P., Z.H. and J.P. are employed by Diagnosticum Zrt, a company that provides custom microarray services.

Techniques: Titration, Microarray, Binding Assay, Transformation Assay, Activity Assay