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: PLoS ONE

Article Title: A MicroRNA Signature Predicts Survival in Early Stage Small-Cell Lung Cancer Treated with Surgery and Adjuvant Chemotherapy

doi: 10.1371/journal.pone.0091388

Figure Lengend Snippet: Kaplan-Meier analyses of overall survival (OS), progression-free survival (PFS), distant metastasis-free survival (DMFS) and local-regional control (LRC) according to the microRNA signature in the training data set (42 SCLC patients).

Article Snippet: Hybridization was performed using a custom microRNA microarray panel (CapitalBio, Beijing, China), which included probes in triplicate for 924 mature human and mouse miRNA sequences and eight short oligonucleotides that possessed no homology to any known RNA sequence as external controls.

Techniques: Control

Journal: PLoS ONE

Article Title: A MicroRNA Signature Predicts Survival in Early Stage Small-Cell Lung Cancer Treated with Surgery and Adjuvant Chemotherapy

doi: 10.1371/journal.pone.0091388

Figure Lengend Snippet: (C) Correlation between expression of U6 RNA by qRT-PCR and log 2-transformed global mean array expression. (D) Expression of U6 RNA in human normal lung (NL, n = 3) and small-cell lung cancer (SCLC, n = 42) samples by microarray method. Whiskers depict the 10 and 90 percentiles. p value is calculated by the Mann-Whitney U test.

Article Snippet: Hybridization was performed using a custom microRNA microarray panel (CapitalBio, Beijing, China), which included probes in triplicate for 924 mature human and mouse miRNA sequences and eight short oligonucleotides that possessed no homology to any known RNA sequence as external controls.

Techniques: Expressing, Quantitative RT-PCR, Transformation Assay, Microarray, MANN-WHITNEY

Journal: PLoS ONE

Article Title: A MicroRNA Signature Predicts Survival in Early Stage Small-Cell Lung Cancer Treated with Surgery and Adjuvant Chemotherapy

doi: 10.1371/journal.pone.0091388

Figure Lengend Snippet: Kaplan-Meier analyses of overall survival (OS), progression-free survival (PFS), distant metastasisfree survival (DMFS) and local-regional control (LRC) according to the microRNA signature in the testing data set (40 SCLC patients).

Article Snippet: Hybridization was performed using a custom microRNA microarray panel (CapitalBio, Beijing, China), which included probes in triplicate for 924 mature human and mouse miRNA sequences and eight short oligonucleotides that possessed no homology to any known RNA sequence as external controls.

Techniques: Control

Journal: iScience

Article Title: Combination of serum human satellite RNA and miR-21-5p levels as a biomarker for pancreatic cancer

doi: 10.1016/j.isci.2023.106021

Figure Lengend Snippet:

Article Snippet: MicroRNA microarray analysis was performed using microRNA microarrays (CosmoBio, Tokyo, Japan).

Techniques: Microarray, Software

Journal: Journal of Allergy

Article Title: How Can Microarrays Unlock Asthma?

doi: 10.1155/2012/241314

Figure Lengend Snippet: List of a number companies currently providing miRNA microarray technology.

Article Snippet: LC Sciences , V17.0 Human microRNA Microarray , http://www.lcsciences.com/.

Techniques: Microarray

Journal: PLoS ONE

Article Title: Coordinated miRNA/mRNA Expression Profiles for Understanding Breed-Specific Metabolic Characters of Liver between Erhualian and Large White Pigs

doi: 10.1371/journal.pone.0038716

Figure Lengend Snippet: Differentially expressed miRNAs in the liver between Large White and Erhualian piglets detected with deep sequencing compared to microarray and RT-PCR validation.

Article Snippet: The pig microRNA microarray was obtained from LC Sciences (Houston, USA) and contains 238 unique probes that were complementary to all mature miRNAs of pig in miRBase release 16.0.

Techniques: Sequencing, Microarray

Journal: PLoS ONE

Article Title: Coordinated miRNA/mRNA Expression Profiles for Understanding Breed-Specific Metabolic Characters of Liver between Erhualian and Large White Pigs

doi: 10.1371/journal.pone.0038716

Figure Lengend Snippet: Differentially expressed miRNAs in the liver between Large White and Erhualian piglets detected with microarray compared to the deep sequencing and RT-qPCR validation.

Article Snippet: The pig microRNA microarray was obtained from LC Sciences (Houston, USA) and contains 238 unique probes that were complementary to all mature miRNAs of pig in miRBase release 16.0.

Techniques: Microarray, Sequencing