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LC Sciences microrna microarray service
$MiRNA profiling by <t>microarray</t> after nucleo-cytoplasmic fractionation of neurons. (A) qRT-PCR analysis of marker genes to validate the fractionation protocol. The fold enrichment (y-axis) of marker genes in the nucleus was calculated by the 2 −dCt [2 −(NUC Ct−CYT Ct) ] method. Bar plots show mean ± standard deviation ( SD ; n = 3). Statistical significance was determined using Student's t -test with Bonferroni correction ( * p < 0.05; ** p < 0.01). (B) Northern blot analysis of the nuclear marker U6 snRNA in nuclear and cytoplasmic fractions. Intensity of the signal was quantified using ImageJ. (C) Detection of nuclear (HDAC2, histone deacetylase 2) and cytoplasmic (beta-Actin) marker proteins in the subcellular fractions using Western blotting assay. Whole cell lysate was used as an input sample. (D) Comparison of different biological replicates from microarray experiments. Pearson's correlation coefficients between indicated samples are shown. Data on gray background represents correlation coefficients for biological replicates from the same cellular fraction. (E) Distribution of miRNA expression in the nucleus and the cytoplasm. Scatterplot of log 2 transformed signal intensity values for miRNAs from nuclear (x-axis) and cytoplasmic (y-axis) fractions (267). Dots above the diagonal indicate cytoplasmic enrichment, below, nuclear enrichment of the respective miRNAs.$
Microrna Microarray Service, supplied by LC Sciences, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Article Title: A comprehensive characterization of the nuclear microRNA repertoire of post-mitotic neurons

Journal: Frontiers in Molecular Neuroscience

doi: 10.3389/fnmol.2013.00043

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

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

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

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

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).

Figure Legend 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).

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

Expressing:

Article Title: MicroRNAs in HIV-Associated Nephropathy (HIVAN)
Article Snippet: RNA extraction microRNA microarray Total RNA was extracted using Trizol (Invitrogen), according to the manufacturer’s instructions. .. Expression of 300 miRNAs (Sanger Version 16.0) was analyzed by microRNA Microarray Service, LC Sciences LLC, Houston, TX. ..

Article Title: MicroRNA (miRNA) Expression is Regulated by Butyrate-Induced Epigenetic Modulation of Gene Expression in Bovine Cells
Article Snippet: The concentration of the total RNA was determined with a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Rockland, DE) and RNA integrity was verified with a Bioanalyzer 1000 (Agilent, Palo Alto, CA). .. microarray MicroRNA microarray service supplied by LC sciences was used for genome-wide miRNA expression profiling. .. LC Sciences (www.lcsciences. com) provides a genome-wide miRNA (miRNA) expression profiling service using μParaflo® technology and proprietary probe design, which enable highly sensitive and specific direct detection of miRNAs.

Article Title: MicroRNA-638 is highly expressed in human vascular smooth muscle cells and inhibits PDGF-BB-induced cell proliferation and migration through targeting orphan nuclear receptor NOR1
Article Snippet: .. Microarray analysis of miRNA expression RNAs obtained from human aortic SMCs treated with PDGF-BB (20 ng/mL) at 0, 3, 6, and 24 h were subjected to the MicroRNA Microarray Service (LC Sciences, Houston, TX, USA). ..

Microarray:

Article Title: TWIST1-induced microRNA-424 reversibly drives mesenchymal programming while inhibiting tumor initiation
Article Snippet: .. MicroRNA microarray and next generation RNA sequencing 10 μg total RNA was isolated using the miRNeasy Mini Kit (Qiagen) and was submitted in triplicate to LC Sciences for microRNA microarray services and data analysis using miRBase v15.0. ..

Article Title: Remote postconditioning ameliorates stroke damage by preventing let-7a and miR-143 up-regulation
Article Snippet: Total RNA from brain tissues was extracted with Trizol following supplier's instruction (TRI Reagent® - Sigma) and RNA quality was assessed using a Thermo ScientificTM NanoDropTM One Microvolume UV-Vis Spectrophotometer. .. RNA samples were sent to LC Sciences (Houston, Texas, USA), a global biotechnology company that is provided with a microRNA microarray service. .. miRNA microarray analysis including separation, quality control, labelling, hybridization and scanning was performed by LC Sciences (Houston, TX, USA) on brain samples collected as above.

Article Title: MicroRNA-638 is highly expressed in human vascular smooth muscle cells and inhibits PDGF-BB-induced cell proliferation and migration through targeting orphan nuclear receptor NOR1
Article Snippet: Human aortic SMCs were purchased from Lonza and cultured as previously described. .. RNAs obtained from human aortic SMCs treated with PDGF-BB (20 ng/mL) at 0, 3, 6, and 24 h were subjected to the MicroRNA Microarray Service (LC Sciences, Houston, TX, USA). .. PCR analysis for miR-638 was performed using the primers (forward: GAG AGG ATC CTG CCG CAG ATC GCT G; reverse: GAG TAA GCT TCA GGG AGT CCT CTG CC). miRNAs and mRNAs were isolated with the miRNeasy Mini Kit (Qiagen) and the RNeasy kit (Qiagen).

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

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