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  • 99
    Thermo Fisher genechip expression eukaryotic poly a rna control kit
    Genechip Expression Eukaryotic Poly A Rna Control Kit, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Millipore mrna
    <t>CHOP</t> functions a transcription repressor in myoblasts. (A) A retrovirus encoding a chimera Engrailed-CHOP protein or a retrovirus containing the parental vector was used to infect C2C12 myoblasts. Infected cells were grown in GM and in DM for the indicated time periods and proteins were analyzed by Western blot (left panel). Infected myoblasts were grown in DM for 48 hours and were immunostained with an anti-MyHC antibody (MF20) (right panel). MyHC staining is in red and DAPI is in blue. Percentage of nuclei in myotubes was calculated from three independent experiments. Mean values and standard errors are presented. Bar, 50 µm. (B) Infected cells described in A were grown in DM for 8 hours and were analyzed by immunostaining with antibodies directed against CHOP and MyoD. Control infected cells (left panel) and Engrailed-CHOP infected cells (right panel). Percentage of MyoD-positive nuclei relative to the total number of nuclei was calculated in three independent experiments. Mean values and standard errors are presented. Bar, 50 µm. (C) C2C12 infected cells as in A were grown in DM for 8 hours and total RNA was then extracted. MyoD <t>mRNA</t> levels were analyzed by semi-quantitative RT-PCR and quantified by the posphoimager.
    Mrna, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 2455 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher messenger rna mrna expression data
    Expression analysis of genes undergoing hypomethylation during RBL to LCL conversion . (a) Expression analysis of selected genes in RBLs and matching LCLs. Error bars represent the standard deviation obtained from six independent measurements. (b) Heatmap showing the relative expression of the 256 genes hypomethylated in B cells with respect to other cell and tissue types. Expression data from <t>Affymetrix</t> <t>mRNA</t> expression analysis with 73 normal human tissues [ 36 ]. (c) Heatmap showing the relative expression of the 256 genes hypomethylated in B cells with respect to LCLs. Expression data obtained from GSE26212 [ 16 ].
    Messenger Rna Mrna Expression Data, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 83/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Arraystar messenger rna mrna expression
    The enrichment Gene Ontology (GO) terms of differentially expressed messenger <t>RNA</t> <t>(mRNA)</t> genes in lung adenocarcinoma (LAD) without lymphatic metastasis compared to adjacent non‐tumor (ANT) lung tissues. Biological process (BP), cellular component (CC) and molecular function (MF) of ( a ) upregulated and ( b ) downregulated mRNAs ( P
    Messenger Rna Mrna Expression, supplied by Arraystar, used in various techniques. Bioz Stars score: 84/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Roche messenger rna mrna expression
    Renin and Collagen I Messenger <t>RNA</t> Expression
    Messenger Rna Mrna Expression, supplied by Roche, used in various techniques. Bioz Stars score: 98/100, based on 45 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    TaKaRa messenger rna mrna expression
    Messenger ribonucleic acid <t>(mRNA)</t> expression of hypoxia-inducible factor (HIF)-1α, p67-phox, senescence marker protein-30 (SMP30), connective tissue growth factor (CTGF), monocyte chemotactic protein-1 (MCP-1) and peroxisome proliferator-activated receptor-gamma coactivator-1α (PGC-1α). Relative expression of HIF-1 α, p67-phox , SMP30 , CTGF , MCP-1 and PGC-1 α in whole kidney were determined by reverse transcription polymerase chain reaction. mRNA content of wild-type (WT) control (Cont) mice was designated as 1.0. Values are means ± standard error; † P
    Messenger Rna Mrna Expression, supplied by TaKaRa, used in various techniques. Bioz Stars score: 93/100, based on 412 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Bio-Rad messenger rna mrna expression
    Effects of ROCK1 and ZIPK knockdown on IL-6 and IL-1β <t>mRNA</t> expression and IL-6 protein secretion. (A) CASMCs were transfected with siRNA to ZIPK or ROCK1 or with negative control siRNA. Cells were lysed 48 h later for <t>qRT-PCR</t> to quantify IL-6 and IL-1β mRNA levels. Values represent means ± SEM ( n = 7 for IL-6 and n = 6 for IL-1β). *significantly different from control (p
    Messenger Rna Mrna Expression, supplied by Bio-Rad, used in various techniques. Bioz Stars score: 94/100, based on 13 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Gallus BioPharmaceuticals messenger rna mrna expression
    Effects of ROCK1 and ZIPK knockdown on IL-6 and IL-1β <t>mRNA</t> expression and IL-6 protein secretion. (A) CASMCs were transfected with siRNA to ZIPK or ROCK1 or with negative control siRNA. Cells were lysed 48 h later for <t>qRT-PCR</t> to quantify IL-6 and IL-1β mRNA levels. Values represent means ± SEM ( n = 7 for IL-6 and n = 6 for IL-1β). *significantly different from control (p
    Messenger Rna Mrna Expression, supplied by Gallus BioPharmaceuticals, used in various techniques. Bioz Stars score: 79/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    NanoString Technologies Inc messenger rna mrna expression
    Effects of ROCK1 and ZIPK knockdown on IL-6 and IL-1β <t>mRNA</t> expression and IL-6 protein secretion. (A) CASMCs were transfected with siRNA to ZIPK or ROCK1 or with negative control siRNA. Cells were lysed 48 h later for <t>qRT-PCR</t> to quantify IL-6 and IL-1β mRNA levels. Values represent means ± SEM ( n = 7 for IL-6 and n = 6 for IL-1β). *significantly different from control (p
    Messenger Rna Mrna Expression, supplied by NanoString Technologies Inc, used in various techniques. Bioz Stars score: 79/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Illumina Inc messenger rna mrna expression
    ADORA2A methylation and A2aR <t>mRNA</t> expression in leucocyte subtypes. A) Mean methylation of CD8 + T, CD4 + T, Treg, B cells, and monocytes as well as HPV-positive and HPV-negative cell lines at different loci within ADORA2A targeted by beads from the <t>Infinium</t> HumanMethylation450 BeadChip. B) A2aR mRNA expression in monocytes, B, CD4 + , and CD8 + T cells. Asteriks imply a significant difference between two groups (*: p°
    Messenger Rna Mrna Expression, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 87/100, based on 19 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Illumina Inc differential expression messenger rna mrna
    ADORA2A methylation and A2aR <t>mRNA</t> expression in leucocyte subtypes. A) Mean methylation of CD8 + T, CD4 + T, Treg, B cells, and monocytes as well as HPV-positive and HPV-negative cell lines at different loci within ADORA2A targeted by beads from the <t>Infinium</t> HumanMethylation450 BeadChip. B) A2aR mRNA expression in monocytes, B, CD4 + , and CD8 + T cells. Asteriks imply a significant difference between two groups (*: p°
    Differential Expression Messenger Rna Mrna, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 89/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    CellSearch mrna expression
    ADORA2A methylation and A2aR <t>mRNA</t> expression in leucocyte subtypes. A) Mean methylation of CD8 + T, CD4 + T, Treg, B cells, and monocytes as well as HPV-positive and HPV-negative cell lines at different loci within ADORA2A targeted by beads from the <t>Infinium</t> HumanMethylation450 BeadChip. B) A2aR mRNA expression in monocytes, B, CD4 + , and CD8 + T cells. Asteriks imply a significant difference between two groups (*: p°
    Mrna Expression, supplied by CellSearch, used in various techniques. Bioz Stars score: 99/100, based on 12 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    4Gene mrna expression
    The <t>mRNA</t> expression of IL - <t>17A</t> with the mRNA expression of IL - 4 , cytokine IL-4 and SCS values among different genotypes in Sanhe Cattle. a Relative mRNA expression of 3 genotypes of SNP in IL - 17A gene. b Relative mRNA expression of 3 genotypes of SNP in IL - 17A in association with IL-4 gene. c Comparison of the genotypes with respect to SCS. d Comparison of the 3 genotypes with respect to the IL-4 cytokines
    Mrna Expression, supplied by 4Gene, used in various techniques. Bioz Stars score: 93/100, based on 69 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Agilent technologies mrna expression
    Venn diagram of overlapping <t>mRNA</t> and <t>lncRNA</t> derived from three group comparisons. a Differentially expressed mRNAs are represented on this Venn diagram, showing either distinct or overlapping relationship with depression or resiliency phenotype. b The diagram represents the unique and overlapping phenotypic association of differentially expressed lncRNA with resiliency or susceptibility to develop depression
    Mrna Expression, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 99/100, based on 503 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher mrna expression
    3’UTR target analysis for methylation sensitive <t>miRNA</t> ( a ) Scatter plot of the number of miRNAs predicted to target the <t>mRNA</t> (Y axis) vs. the maximum inverse correlation exhibited between the mRNA the miRNAs (X axis). Labeled mRNAs from the top 5% are significantly associated with poor OS when over-expressed in tumors. ( b ) A radial bipartite graph showing mRNAs highlighted in (a) with miRNA interactions. Only genes with significant associations with OS are depicted. Edge thickness is proportional to both inverse expression correlation and the over-representation of predicted mRNA targets. ( c ) Gene ontology analysis for the 1,250 over-represented target mRNAs with significant inverse correlation to the 67 methylation sensitive miRNAs.(*p
    Mrna Expression, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 14009 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    SLIT2 LTD mrna expression
    Upregulation of miR-218 reduces Robo1 expression through the inactivation of <t>Slit2-Robo1</t> signaling. (A and B) The U87 cells were treated with control, NC and miR-218 mimics, and the levels of Robo1 and Slit2 <t>mRNA</t> were measured by quantitative polymerase chain reaction.(C) The level of Robo1 and Slit2 protein expression in the U87 cells was measured by western blot analysis. * P
    Mrna Expression, supplied by SLIT2 LTD, used in various techniques. Bioz Stars score: 99/100, based on 62 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Cytox mrna expression
    Upregulation of miR-218 reduces Robo1 expression through the inactivation of <t>Slit2-Robo1</t> signaling. (A and B) The U87 cells were treated with control, NC and miR-218 mimics, and the levels of Robo1 and Slit2 <t>mRNA</t> were measured by quantitative polymerase chain reaction.(C) The level of Robo1 and Slit2 protein expression in the U87 cells was measured by western blot analysis. * P
    Mrna Expression, supplied by Cytox, used in various techniques. Bioz Stars score: 94/100, based on 12 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Human Protein Atlas mrna expression
    Genetic alteration and gene expression of <t>NOX</t> family in GC. Notes: ( A ) Alteration frequency analysis of NOX genes in GC using cBioPortal. ( B ) Relative expression differences of NOX family genes in GC using Human Protein Atlas database. ( C ) Comparison of NOX1, NOX2, NOX4, NOX5, DUOX1, DUOX2 <t>mRNA</t> expression in gastric normal (left plot n=80) and cancer tissue (right plot n=80) in Cui dataset using Oncomine. Abbreviations: GC, gastric cancer; NADPH, nicotinamide adenine dinucleotide phosphate; NOX, NADPH oxidases.
    Mrna Expression, supplied by Human Protein Atlas, used in various techniques. Bioz Stars score: 99/100, based on 64 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    VANGL2 LTD mrna expression
    Active β-catenin, Prickle1 and <t>Vangl2</t> are differently expressed in neuroblastoma cell lines. a Protein expression of active, de-phoshorylated β-catenin, the canonical Wnt/β-catenin target gene Axin2 and b . total β-catenin in neuroblastoma cell lines. SK-N-BE (2), SK-N-DZ, IMR-32 and Kelly are MYCN amplified neuroblastoma cells with high MycN expression. SH-SY5Y, SK-N-SH and SK-N-FI are non- MYCN amplified neuroblastoma cells expressing relatively low levels of MycN whereas, SK-N-AS and SHEP-1 do not show any MycN expression [ 33 ] c . Quantified protein expression (adjusted to β-actin) of Prickle1 and Vangl2 in neuroblastoma cell lines. Proteins were determined with western blotting. d <t>mRNA</t> expression in neuroblastoma cell lines SK-N-BE (2), SK-N-DZ, SK-N-AS, SH-EP1 and SH-SY5Y, assessed by quantitative real-time PCR, the data displayed is the mean ± S.D. of three determinations
    Mrna Expression, supplied by VANGL2 LTD, used in various techniques. Bioz Stars score: 99/100, based on 40 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Epigenomics mrna expression
    Active β-catenin, Prickle1 and <t>Vangl2</t> are differently expressed in neuroblastoma cell lines. a Protein expression of active, de-phoshorylated β-catenin, the canonical Wnt/β-catenin target gene Axin2 and b . total β-catenin in neuroblastoma cell lines. SK-N-BE (2), SK-N-DZ, IMR-32 and Kelly are MYCN amplified neuroblastoma cells with high MycN expression. SH-SY5Y, SK-N-SH and SK-N-FI are non- MYCN amplified neuroblastoma cells expressing relatively low levels of MycN whereas, SK-N-AS and SHEP-1 do not show any MycN expression [ 33 ] c . Quantified protein expression (adjusted to β-actin) of Prickle1 and Vangl2 in neuroblastoma cell lines. Proteins were determined with western blotting. d <t>mRNA</t> expression in neuroblastoma cell lines SK-N-BE (2), SK-N-DZ, SK-N-AS, SH-EP1 and SH-SY5Y, assessed by quantitative real-time PCR, the data displayed is the mean ± S.D. of three determinations
    Mrna Expression, supplied by Epigenomics, used in various techniques. Bioz Stars score: 94/100, based on 18 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Syntaxin mrna expression
    Expressions of SNARE complex in submandibular glands ( A ) Expression of <t>VAMP-2,</t> syntaxin-2, syntaxin-4 , and SNAP-23 mRNAs using reverse-transcription PCR (RT-PCR). Relative VAMP-2 ( B ) and syntaxin-4 ( C ) <t>mRNA</t> expression in control and transplanted glands was determined by qPCR. ( D ) Representative co-immunoprecipitation results in control and transplanted glands using VAMP-2 antibody. The band intensities of actin, syntaxin-4, Igκ, myosin regulatory light polypeptide 9, and myosin light polypeptide 6 were normalized to VAMP-2 expression. Quantitative analysis of actin ( E ), syntaxin-4 ( F ), Igκ ( G ), myosin regulatory light polypeptide 9 ( H ), and myosin light polypeptide 6 ( I ) interaction with VAMP-2 in control and transplanted glands. Values are the mean ± S.D. from six independent experiments. * P
    Mrna Expression, supplied by Syntaxin, used in various techniques. Bioz Stars score: 94/100, based on 51 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Graph Pad Software Inc mrna expression
    Expressions of SNARE complex in submandibular glands ( A ) Expression of <t>VAMP-2,</t> syntaxin-2, syntaxin-4 , and SNAP-23 mRNAs using reverse-transcription PCR (RT-PCR). Relative VAMP-2 ( B ) and syntaxin-4 ( C ) <t>mRNA</t> expression in control and transplanted glands was determined by qPCR. ( D ) Representative co-immunoprecipitation results in control and transplanted glands using VAMP-2 antibody. The band intensities of actin, syntaxin-4, Igκ, myosin regulatory light polypeptide 9, and myosin light polypeptide 6 were normalized to VAMP-2 expression. Quantitative analysis of actin ( E ), syntaxin-4 ( F ), Igκ ( G ), myosin regulatory light polypeptide 9 ( H ), and myosin light polypeptide 6 ( I ) interaction with VAMP-2 in control and transplanted glands. Values are the mean ± S.D. from six independent experiments. * P
    Mrna Expression, supplied by Graph Pad Software Inc, used in various techniques. Bioz Stars score: 91/100, based on 46 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Illumina Inc mrna expression data
    Integrative <t>miRNA–mRNA</t> analysis. ( A ) Illustration of the analysis workflow. ( B ) Tallies of significant miRNA and mRNA probes after filtering using Tukey's P -value (
    Mrna Expression Data, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 141 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Illumina Inc mrna expression analysis
    Integrative <t>miRNA–mRNA</t> analysis. ( A ) Illustration of the analysis workflow. ( B ) Tallies of significant miRNA and mRNA probes after filtering using Tukey's P -value (
    Mrna Expression Analysis, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 93/100, based on 30 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Illumina Inc truseq messenger rna mrna
    Gene expression changes in CD28- vs CD86-silenced cells are consistent with regulation of both distinct and common pathways, including expression of IRF4. (A) Gene set enrichment analysis showing upregulated (top) and downregulated (bottom) gene sets in shCD28- (blue) and shCD86-treated (red) myeloma cells. For each gene set, the enrichment score is shown above the ranked change in gene expression, where genes that overlap the gene set are denoted by blue and red ticks for shCD28 and shCD86, respectively. (B) qRT-PCR showing IRF4 <t>mRNA</t> levels when CD28 or CD86 was silenced in MM.1s or 8226 cells. (C) Representative western blots showing IRF4 levels with silencing of CD28 or CD86 in cell lines indicated at different time points. (D) Integrin levels were measured via qRT-PCR ( ITGB7 and ITGB1 ; left). Representative histograms showing ITGβ1 and ITGβ7 on day 4 after shRNA treatment (right). For qRT-PCR, all data are normalized to β-actin as an endogenous control and then compared relative to mRNA levels in pLKO.1 empty vector control. <t>RNA</t> was extracted at day 3 postinfection. Data shown are mean ± SEM of at least 3 independent experiments. Histograms showing surface levels of indicated molecules. Gray histograms at left represent unstained or isotype controls. Flow cytometry data shown are from day 4 postinfection with lentiviral vectors. Flow cytometry and western blot data shown are representative of at least 3 independent experiments. (E) Cell adhesion 3 days postinfection with lentivirus containing the indicated shRNA. Myeloma cells stained with calcein AM were cocultured with HS-5 cells for 2 hours. Fluorescence was measured (485/528 emission/excitation) with BioTek Synergy H1 multiwell plate reader, and data are presented as fluorescence relative to pLKO.1 controls (mean ± SEM). Prewash readings were taken to ensure similar numbers of live cells were added to each well. All samples were plated in triplicate. Data are mean of 3 independent experiments. GAPDH, glyceraldehyde-3-phosphate dehydrogenase; GX, gene expression changes; RFU, relative fluorescence unit.
    Truseq Messenger Rna Mrna, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Promega messenger rna expression levels
    Gene expression changes in CD28- vs CD86-silenced cells are consistent with regulation of both distinct and common pathways, including expression of IRF4. (A) Gene set enrichment analysis showing upregulated (top) and downregulated (bottom) gene sets in shCD28- (blue) and shCD86-treated (red) myeloma cells. For each gene set, the enrichment score is shown above the ranked change in gene expression, where genes that overlap the gene set are denoted by blue and red ticks for shCD28 and shCD86, respectively. (B) qRT-PCR showing IRF4 <t>mRNA</t> levels when CD28 or CD86 was silenced in MM.1s or 8226 cells. (C) Representative western blots showing IRF4 levels with silencing of CD28 or CD86 in cell lines indicated at different time points. (D) Integrin levels were measured via qRT-PCR ( ITGB7 and ITGB1 ; left). Representative histograms showing ITGβ1 and ITGβ7 on day 4 after shRNA treatment (right). For qRT-PCR, all data are normalized to β-actin as an endogenous control and then compared relative to mRNA levels in pLKO.1 empty vector control. <t>RNA</t> was extracted at day 3 postinfection. Data shown are mean ± SEM of at least 3 independent experiments. Histograms showing surface levels of indicated molecules. Gray histograms at left represent unstained or isotype controls. Flow cytometry data shown are from day 4 postinfection with lentiviral vectors. Flow cytometry and western blot data shown are representative of at least 3 independent experiments. (E) Cell adhesion 3 days postinfection with lentivirus containing the indicated shRNA. Myeloma cells stained with calcein AM were cocultured with HS-5 cells for 2 hours. Fluorescence was measured (485/528 emission/excitation) with BioTek Synergy H1 multiwell plate reader, and data are presented as fluorescence relative to pLKO.1 controls (mean ± SEM). Prewash readings were taken to ensure similar numbers of live cells were added to each well. All samples were plated in triplicate. Data are mean of 3 independent experiments. GAPDH, glyceraldehyde-3-phosphate dehydrogenase; GX, gene expression changes; RFU, relative fluorescence unit.
    Messenger Rna Expression Levels, supplied by Promega, used in various techniques. Bioz Stars score: 80/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher hugus mrna expression
    Gene expression changes in CD28- vs CD86-silenced cells are consistent with regulation of both distinct and common pathways, including expression of IRF4. (A) Gene set enrichment analysis showing upregulated (top) and downregulated (bottom) gene sets in shCD28- (blue) and shCD86-treated (red) myeloma cells. For each gene set, the enrichment score is shown above the ranked change in gene expression, where genes that overlap the gene set are denoted by blue and red ticks for shCD28 and shCD86, respectively. (B) qRT-PCR showing IRF4 <t>mRNA</t> levels when CD28 or CD86 was silenced in MM.1s or 8226 cells. (C) Representative western blots showing IRF4 levels with silencing of CD28 or CD86 in cell lines indicated at different time points. (D) Integrin levels were measured via qRT-PCR ( ITGB7 and ITGB1 ; left). Representative histograms showing ITGβ1 and ITGβ7 on day 4 after shRNA treatment (right). For qRT-PCR, all data are normalized to β-actin as an endogenous control and then compared relative to mRNA levels in pLKO.1 empty vector control. <t>RNA</t> was extracted at day 3 postinfection. Data shown are mean ± SEM of at least 3 independent experiments. Histograms showing surface levels of indicated molecules. Gray histograms at left represent unstained or isotype controls. Flow cytometry data shown are from day 4 postinfection with lentiviral vectors. Flow cytometry and western blot data shown are representative of at least 3 independent experiments. (E) Cell adhesion 3 days postinfection with lentivirus containing the indicated shRNA. Myeloma cells stained with calcein AM were cocultured with HS-5 cells for 2 hours. Fluorescence was measured (485/528 emission/excitation) with BioTek Synergy H1 multiwell plate reader, and data are presented as fluorescence relative to pLKO.1 controls (mean ± SEM). Prewash readings were taken to ensure similar numbers of live cells were added to each well. All samples were plated in triplicate. Data are mean of 3 independent experiments. GAPDH, glyceraldehyde-3-phosphate dehydrogenase; GX, gene expression changes; RFU, relative fluorescence unit.
    Hugus Mrna Expression, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 79/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher mrna expression microarray
    Gene expression changes in CD28- vs CD86-silenced cells are consistent with regulation of both distinct and common pathways, including expression of IRF4. (A) Gene set enrichment analysis showing upregulated (top) and downregulated (bottom) gene sets in shCD28- (blue) and shCD86-treated (red) myeloma cells. For each gene set, the enrichment score is shown above the ranked change in gene expression, where genes that overlap the gene set are denoted by blue and red ticks for shCD28 and shCD86, respectively. (B) qRT-PCR showing IRF4 <t>mRNA</t> levels when CD28 or CD86 was silenced in MM.1s or 8226 cells. (C) Representative western blots showing IRF4 levels with silencing of CD28 or CD86 in cell lines indicated at different time points. (D) Integrin levels were measured via qRT-PCR ( ITGB7 and ITGB1 ; left). Representative histograms showing ITGβ1 and ITGβ7 on day 4 after shRNA treatment (right). For qRT-PCR, all data are normalized to β-actin as an endogenous control and then compared relative to mRNA levels in pLKO.1 empty vector control. <t>RNA</t> was extracted at day 3 postinfection. Data shown are mean ± SEM of at least 3 independent experiments. Histograms showing surface levels of indicated molecules. Gray histograms at left represent unstained or isotype controls. Flow cytometry data shown are from day 4 postinfection with lentiviral vectors. Flow cytometry and western blot data shown are representative of at least 3 independent experiments. (E) Cell adhesion 3 days postinfection with lentivirus containing the indicated shRNA. Myeloma cells stained with calcein AM were cocultured with HS-5 cells for 2 hours. Fluorescence was measured (485/528 emission/excitation) with BioTek Synergy H1 multiwell plate reader, and data are presented as fluorescence relative to pLKO.1 controls (mean ± SEM). Prewash readings were taken to ensure similar numbers of live cells were added to each well. All samples were plated in triplicate. Data are mean of 3 independent experiments. GAPDH, glyceraldehyde-3-phosphate dehydrogenase; GX, gene expression changes; RFU, relative fluorescence unit.
    Mrna Expression Microarray, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 98/100, based on 28 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Agilent technologies pik3ca mrna expression
    <t>PIK3CA</t> expression level increases from corresponding primary to metastatic lesions. ( a ) The PIK3CA <t>mRNA</t> expression level increases significantly from the primary tumors to metastatic lesions measured within same patient. ( b ) Binary directional shift in PIK3CA expression level in the metastasis compared to the primary tumor. The absence of mutation is most likely to increase PIK3CA expression towards metastatic state, while half of the cases with mutations also display reduced PIK3CA expression in the metastatic lesions. Number of cases is indicated as affected cases/total cases in each group. ( c ) The PI3K mRNA signature score defined by Gustafson et al . 29 and ( d ) expression of p-AKT/AKT comparing the paired samples of corresponding primary and metastatic tumors. For simplicity, first metastatic lesion (M1) was used as comparison when multiple metastases were available. Statistical test: Mann-Whitney U test.
    Pik3ca Mrna Expression, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 89/100, based on 14 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    fluidigm mrna expression assay
    <t>PIK3CA</t> expression level increases from corresponding primary to metastatic lesions. ( a ) The PIK3CA <t>mRNA</t> expression level increases significantly from the primary tumors to metastatic lesions measured within same patient. ( b ) Binary directional shift in PIK3CA expression level in the metastasis compared to the primary tumor. The absence of mutation is most likely to increase PIK3CA expression towards metastatic state, while half of the cases with mutations also display reduced PIK3CA expression in the metastatic lesions. Number of cases is indicated as affected cases/total cases in each group. ( c ) The PI3K mRNA signature score defined by Gustafson et al . 29 and ( d ) expression of p-AKT/AKT comparing the paired samples of corresponding primary and metastatic tumors. For simplicity, first metastatic lesion (M1) was used as comparison when multiple metastases were available. Statistical test: Mann-Whitney U test.
    Mrna Expression Assay, supplied by fluidigm, used in various techniques. Bioz Stars score: 79/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Illumina Inc messenger rna expression microarray
    <t>PIK3CA</t> expression level increases from corresponding primary to metastatic lesions. ( a ) The PIK3CA <t>mRNA</t> expression level increases significantly from the primary tumors to metastatic lesions measured within same patient. ( b ) Binary directional shift in PIK3CA expression level in the metastasis compared to the primary tumor. The absence of mutation is most likely to increase PIK3CA expression towards metastatic state, while half of the cases with mutations also display reduced PIK3CA expression in the metastatic lesions. Number of cases is indicated as affected cases/total cases in each group. ( c ) The PI3K mRNA signature score defined by Gustafson et al . 29 and ( d ) expression of p-AKT/AKT comparing the paired samples of corresponding primary and metastatic tumors. For simplicity, first metastatic lesion (M1) was used as comparison when multiple metastases were available. Statistical test: Mann-Whitney U test.
    Messenger Rna Expression Microarray, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 80/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    CHOP functions a transcription repressor in myoblasts. (A) A retrovirus encoding a chimera Engrailed-CHOP protein or a retrovirus containing the parental vector was used to infect C2C12 myoblasts. Infected cells were grown in GM and in DM for the indicated time periods and proteins were analyzed by Western blot (left panel). Infected myoblasts were grown in DM for 48 hours and were immunostained with an anti-MyHC antibody (MF20) (right panel). MyHC staining is in red and DAPI is in blue. Percentage of nuclei in myotubes was calculated from three independent experiments. Mean values and standard errors are presented. Bar, 50 µm. (B) Infected cells described in A were grown in DM for 8 hours and were analyzed by immunostaining with antibodies directed against CHOP and MyoD. Control infected cells (left panel) and Engrailed-CHOP infected cells (right panel). Percentage of MyoD-positive nuclei relative to the total number of nuclei was calculated in three independent experiments. Mean values and standard errors are presented. Bar, 50 µm. (C) C2C12 infected cells as in A were grown in DM for 8 hours and total RNA was then extracted. MyoD mRNA levels were analyzed by semi-quantitative RT-PCR and quantified by the posphoimager.

    Journal: PLoS ONE

    Article Title: Stress-Induced C/EBP Homology Protein (CHOP) Represses MyoD Transcription to Delay Myoblast Differentiation

    doi: 10.1371/journal.pone.0029498

    Figure Lengend Snippet: CHOP functions a transcription repressor in myoblasts. (A) A retrovirus encoding a chimera Engrailed-CHOP protein or a retrovirus containing the parental vector was used to infect C2C12 myoblasts. Infected cells were grown in GM and in DM for the indicated time periods and proteins were analyzed by Western blot (left panel). Infected myoblasts were grown in DM for 48 hours and were immunostained with an anti-MyHC antibody (MF20) (right panel). MyHC staining is in red and DAPI is in blue. Percentage of nuclei in myotubes was calculated from three independent experiments. Mean values and standard errors are presented. Bar, 50 µm. (B) Infected cells described in A were grown in DM for 8 hours and were analyzed by immunostaining with antibodies directed against CHOP and MyoD. Control infected cells (left panel) and Engrailed-CHOP infected cells (right panel). Percentage of MyoD-positive nuclei relative to the total number of nuclei was calculated in three independent experiments. Mean values and standard errors are presented. Bar, 50 µm. (C) C2C12 infected cells as in A were grown in DM for 8 hours and total RNA was then extracted. MyoD mRNA levels were analyzed by semi-quantitative RT-PCR and quantified by the posphoimager.

    Article Snippet: ShRNA-mediated knockdown of proteins Knockdown of the CHOP protein in myoblasts was achieved by lentiviral infections of 5 viral vectors that express different shRNA directed to CHOP mRNA and were purchased from Sigma-Aldrich (ShRNA MISSION).

    Techniques: Plasmid Preparation, Infection, Western Blot, Staining, Immunostaining, Quantitative RT-PCR

    CHOP represses MyoD transcription. (A) A C2C12 derived cell line expressing a chimera CHOP:ER protein was constructed as is described under “ Materials and Methods ”. (A) Myoblasts were grown in the presence of ethanol or β estradiol (0.1 µM) for 8 hours. Cells were immunostained using anti-MyoD and anti-CHOP antibodies. DAPI in blue, MyoD in green and CHOP in red. Percentage of MyoD-positive nuclei relative to the total number of nuclei was calculated. Bar, 50 µm. (left panel). In another experiment, cells were grown in the presence of ethanol or β estradiol (0.1 µM) for 48 hours and proteins were analyzed by Western blot (right panel). (B) The same cells as above were grown in DM in the presence of ethanol or β estradiol (0.1 µM) for the indicated time periods and mRNA levels of myod and myogenin were determined by semi-quantitative RT-PCR analysis. (C) The same cells as above were grown in DM and in the presence of ethanol or β estradiol for 6 hours in the absence or presence of cycloheximide added to cells one hour before the addition of ethanol or β estradiol. (D) A clone of the above cells (i.e., expressing CHOP:ER) with integrated MyoD reporter gene (6.0 MyoD -nl β Gal) was isolated. These cells were grown in the presence of ethanol or β estradiol for 20 hours. Nuclear expression of β Gal was identified by an enzymatic colorimetric assay, and the expression of CHOP by immunostaining. Arrows point at β Gal-positive nuclei that are CHOP negative. Percentage of β Gal-positive nuclei out of the total number of nuclei was calculated in two independent experiments. Mean values and standard errors are presented. Bar, 50 µm.

    Journal: PLoS ONE

    Article Title: Stress-Induced C/EBP Homology Protein (CHOP) Represses MyoD Transcription to Delay Myoblast Differentiation

    doi: 10.1371/journal.pone.0029498

    Figure Lengend Snippet: CHOP represses MyoD transcription. (A) A C2C12 derived cell line expressing a chimera CHOP:ER protein was constructed as is described under “ Materials and Methods ”. (A) Myoblasts were grown in the presence of ethanol or β estradiol (0.1 µM) for 8 hours. Cells were immunostained using anti-MyoD and anti-CHOP antibodies. DAPI in blue, MyoD in green and CHOP in red. Percentage of MyoD-positive nuclei relative to the total number of nuclei was calculated. Bar, 50 µm. (left panel). In another experiment, cells were grown in the presence of ethanol or β estradiol (0.1 µM) for 48 hours and proteins were analyzed by Western blot (right panel). (B) The same cells as above were grown in DM in the presence of ethanol or β estradiol (0.1 µM) for the indicated time periods and mRNA levels of myod and myogenin were determined by semi-quantitative RT-PCR analysis. (C) The same cells as above were grown in DM and in the presence of ethanol or β estradiol for 6 hours in the absence or presence of cycloheximide added to cells one hour before the addition of ethanol or β estradiol. (D) A clone of the above cells (i.e., expressing CHOP:ER) with integrated MyoD reporter gene (6.0 MyoD -nl β Gal) was isolated. These cells were grown in the presence of ethanol or β estradiol for 20 hours. Nuclear expression of β Gal was identified by an enzymatic colorimetric assay, and the expression of CHOP by immunostaining. Arrows point at β Gal-positive nuclei that are CHOP negative. Percentage of β Gal-positive nuclei out of the total number of nuclei was calculated in two independent experiments. Mean values and standard errors are presented. Bar, 50 µm.

    Article Snippet: ShRNA-mediated knockdown of proteins Knockdown of the CHOP protein in myoblasts was achieved by lentiviral infections of 5 viral vectors that express different shRNA directed to CHOP mRNA and were purchased from Sigma-Aldrich (ShRNA MISSION).

    Techniques: Derivative Assay, Expressing, Construct, Western Blot, Quantitative RT-PCR, Isolation, Enzymatic Colorimetric Assay, Immunostaining

    BCAS2 does not regulate the transcription initiation of Delta but is involved in Delta pre-mRNA splicing. (A) Control of Dl-lacZ (red) in the en > GFP wing disc stained with anti-β-gal antibody. (B) en > GFP , dBCAS2 dsRNA . In the dBCAS2 -depleted posterior compartment, marked by GFP, the expression of Dl-lacZ (red) gives a signal of similar strength as the normal anterior compartment. The expression of GFP and β-galactosidase were merged and displayed in the right panel. Images were taken by confocal microscopy, scale bar, 50 μm. (C). RNA expression of β-galactosidase. RNAs were extracted from wing discs of third instar larvae and subjected to RT-PCR to confirm the RNA expression of β-galactosidase driven by Dl promoter in Act > dBCAS2 dsRNA (lane 2) compared with the control (lane 1). The internal control, rp49 . (D) Schematic diagram of primer design for detecting the intron-containing precursor mRNA (upper) and mRNA of Delta (lower). Primers, exons and introns are denoted with arrowheads, boxes and lines, respectively. (E) Coexpression of dBCAS2 and dBCAS2 dsRNA in larvae can rescue the phenotypes of mRNA decrease and pre-mRNA accumulation caused by dBCAS2 dsRNA . The pre-mRNA and mRNA of Delta were analyzed by quantitative RT-PCR and described in the Materials and Methods. Each genotype was under the control of Act5c-GAL4 driver. White bar: Act5c > +; black bar: Act5c > dBCAS2 dsRNA ; gray bar: Act5c > dBCAS2 dsRNA , dBCAS2 . Data are shown as means and SD relative to the controls from three independent experiments. The P-values was measured by the Student’s t-test. * p

    Journal: PLoS ONE

    Article Title: BCAS2 Regulates Delta-Notch Signaling Activity through Delta Pre-mRNA Splicing in Drosophila Wing Development

    doi: 10.1371/journal.pone.0130706

    Figure Lengend Snippet: BCAS2 does not regulate the transcription initiation of Delta but is involved in Delta pre-mRNA splicing. (A) Control of Dl-lacZ (red) in the en > GFP wing disc stained with anti-β-gal antibody. (B) en > GFP , dBCAS2 dsRNA . In the dBCAS2 -depleted posterior compartment, marked by GFP, the expression of Dl-lacZ (red) gives a signal of similar strength as the normal anterior compartment. The expression of GFP and β-galactosidase were merged and displayed in the right panel. Images were taken by confocal microscopy, scale bar, 50 μm. (C). RNA expression of β-galactosidase. RNAs were extracted from wing discs of third instar larvae and subjected to RT-PCR to confirm the RNA expression of β-galactosidase driven by Dl promoter in Act > dBCAS2 dsRNA (lane 2) compared with the control (lane 1). The internal control, rp49 . (D) Schematic diagram of primer design for detecting the intron-containing precursor mRNA (upper) and mRNA of Delta (lower). Primers, exons and introns are denoted with arrowheads, boxes and lines, respectively. (E) Coexpression of dBCAS2 and dBCAS2 dsRNA in larvae can rescue the phenotypes of mRNA decrease and pre-mRNA accumulation caused by dBCAS2 dsRNA . The pre-mRNA and mRNA of Delta were analyzed by quantitative RT-PCR and described in the Materials and Methods. Each genotype was under the control of Act5c-GAL4 driver. White bar: Act5c > +; black bar: Act5c > dBCAS2 dsRNA ; gray bar: Act5c > dBCAS2 dsRNA , dBCAS2 . Data are shown as means and SD relative to the controls from three independent experiments. The P-values was measured by the Student’s t-test. * p

    Article Snippet: In vivo splicing assays For the detection of mRNA and pre-mRNA in Drosophila , total RNA from imaginal wing discs in 20 third instar larvae was isolated by using TRI reagent (Sigma-Aldrich).

    Techniques: Staining, Expressing, Confocal Microscopy, RNA Expression, Reverse Transcription Polymerase Chain Reaction, Activated Clotting Time Assay, Quantitative RT-PCR

    RT–PCR analysis of HIV-1 mRNA expression. RT–PCR analysis of uncleaved HIV-1 mRNA was carried out using HIV-1 env -specific primers with concomitant amplification of G3PDH. Total RNA was extracted from COS cells transfected with E2-ss- or dsRNAs first, followed by pNL4-3. The relative amounts of HIV-1 transcripts were determined by RT–PCR, as described in Materials and Methods. PCR primers were used to amplify a 529 bp (7072–7600) fragment in HIV-1 transcripts. Lane 1, negative control (no template added); lane 2, relative amount of transcripts in cells transfected with E2-dsRNA; lane 3, relative amount of transcripts in cells transfected with E2-ssRNA; lane 4, relative amount of transcripts in positive control cells transfected with pNL4-3 proviral DNA. The G3PDH RT–PCR was run in parallel to normalize the levels of mRNA in the samples.

    Journal: Nucleic Acids Research

    Article Title: Prevention of HIV-1 infection in human peripheral blood mononuclear cells by specific RNA interference

    doi:

    Figure Lengend Snippet: RT–PCR analysis of HIV-1 mRNA expression. RT–PCR analysis of uncleaved HIV-1 mRNA was carried out using HIV-1 env -specific primers with concomitant amplification of G3PDH. Total RNA was extracted from COS cells transfected with E2-ss- or dsRNAs first, followed by pNL4-3. The relative amounts of HIV-1 transcripts were determined by RT–PCR, as described in Materials and Methods. PCR primers were used to amplify a 529 bp (7072–7600) fragment in HIV-1 transcripts. Lane 1, negative control (no template added); lane 2, relative amount of transcripts in cells transfected with E2-dsRNA; lane 3, relative amount of transcripts in cells transfected with E2-ssRNA; lane 4, relative amount of transcripts in positive control cells transfected with pNL4-3 proviral DNA. The G3PDH RT–PCR was run in parallel to normalize the levels of mRNA in the samples.

    Article Snippet: The reverse transcription and the PCR analysis were performed with total RNA from COS cells (prepared with the GenElute Mammalian Total RNA kit; Sigma) as the template (1 µg/reaction).

    Techniques: Reverse Transcription Polymerase Chain Reaction, Expressing, Amplification, Transfection, Polymerase Chain Reaction, Negative Control, Positive Control

    Expression analysis of genes undergoing hypomethylation during RBL to LCL conversion . (a) Expression analysis of selected genes in RBLs and matching LCLs. Error bars represent the standard deviation obtained from six independent measurements. (b) Heatmap showing the relative expression of the 256 genes hypomethylated in B cells with respect to other cell and tissue types. Expression data from Affymetrix mRNA expression analysis with 73 normal human tissues [ 36 ]. (c) Heatmap showing the relative expression of the 256 genes hypomethylated in B cells with respect to LCLs. Expression data obtained from GSE26212 [ 16 ].

    Journal: Genome Biology

    Article Title: The B cell transcription program mediates hypomethylation and overexpression of key genes in Epstein-Barr virus-associated proliferative conversion

    doi: 10.1186/gb-2013-14-1-r3

    Figure Lengend Snippet: Expression analysis of genes undergoing hypomethylation during RBL to LCL conversion . (a) Expression analysis of selected genes in RBLs and matching LCLs. Error bars represent the standard deviation obtained from six independent measurements. (b) Heatmap showing the relative expression of the 256 genes hypomethylated in B cells with respect to other cell and tissue types. Expression data from Affymetrix mRNA expression analysis with 73 normal human tissues [ 36 ]. (c) Heatmap showing the relative expression of the 256 genes hypomethylated in B cells with respect to LCLs. Expression data obtained from GSE26212 [ 16 ].

    Article Snippet: Thus, we compared normalized Affymetrix mRNA expression data of 73 normal human tissues [ ].

    Techniques: Expressing, Standard Deviation

    The enrichment Gene Ontology (GO) terms of differentially expressed messenger RNA (mRNA) genes in lung adenocarcinoma (LAD) without lymphatic metastasis compared to adjacent non‐tumor (ANT) lung tissues. Biological process (BP), cellular component (CC) and molecular function (MF) of ( a ) upregulated and ( b ) downregulated mRNAs ( P

    Journal: Thoracic Cancer

    Article Title: Microarray expression profile of long non‐coding RNAs in human lung adenocarcinoma

    doi: 10.1111/1759-7714.12845

    Figure Lengend Snippet: The enrichment Gene Ontology (GO) terms of differentially expressed messenger RNA (mRNA) genes in lung adenocarcinoma (LAD) without lymphatic metastasis compared to adjacent non‐tumor (ANT) lung tissues. Biological process (BP), cellular component (CC) and molecular function (MF) of ( a ) upregulated and ( b ) downregulated mRNAs ( P

    Article Snippet: LncRNA and messenger RNA (mRNA) expression in LAD without lymphatic metastasis versus paired adjacent non‐tumor (ANT) lung tissues and LAD with versus without lymphatic metastasis were analyzed using Human LncRNA Arraystar V3.0.

    Techniques:

    The enrichment Gene Ontology (GO) terms of differentially expressed (DE) messenger RNA (mRNA) genes in lung adenocarcinoma (LAD) with and without lymphatic metastasis. Biological process (BP), cellular component (CC), and molecular function (MF) of ( a ) upregulated and ( b ) downregulated mRNAs ( P

    Journal: Thoracic Cancer

    Article Title: Microarray expression profile of long non‐coding RNAs in human lung adenocarcinoma

    doi: 10.1111/1759-7714.12845

    Figure Lengend Snippet: The enrichment Gene Ontology (GO) terms of differentially expressed (DE) messenger RNA (mRNA) genes in lung adenocarcinoma (LAD) with and without lymphatic metastasis. Biological process (BP), cellular component (CC), and molecular function (MF) of ( a ) upregulated and ( b ) downregulated mRNAs ( P

    Article Snippet: LncRNA and messenger RNA (mRNA) expression in LAD without lymphatic metastasis versus paired adjacent non‐tumor (ANT) lung tissues and LAD with versus without lymphatic metastasis were analyzed using Human LncRNA Arraystar V3.0.

    Techniques:

    Long non‐coding RNA (lncRNA) and messenger RNA (mRNA) expression profiles. ( a ) Hierarchical clustering of lncRNA profiles in lung adenocarcinoma (LAD) without lymphatic metastasis (group‐Exp1) compared to adjacent non‐tumor (ANT) lung tissues (group‐ctrl), and ( b ) in LAD with lymphatic metastasis (group‐Exp2) versus LAD without lymphatic metastasis (group‐Exp1). ( c ) Hierarchical clustering of mRNA profiles in group‐Exp1 compared to group‐ctrl, and ( d ) in group‐Exp2 versus group‐Exp1. The expression level increases from green to red (≥ 2‐fold, P

    Journal: Thoracic Cancer

    Article Title: Microarray expression profile of long non‐coding RNAs in human lung adenocarcinoma

    doi: 10.1111/1759-7714.12845

    Figure Lengend Snippet: Long non‐coding RNA (lncRNA) and messenger RNA (mRNA) expression profiles. ( a ) Hierarchical clustering of lncRNA profiles in lung adenocarcinoma (LAD) without lymphatic metastasis (group‐Exp1) compared to adjacent non‐tumor (ANT) lung tissues (group‐ctrl), and ( b ) in LAD with lymphatic metastasis (group‐Exp2) versus LAD without lymphatic metastasis (group‐Exp1). ( c ) Hierarchical clustering of mRNA profiles in group‐Exp1 compared to group‐ctrl, and ( d ) in group‐Exp2 versus group‐Exp1. The expression level increases from green to red (≥ 2‐fold, P

    Article Snippet: LncRNA and messenger RNA (mRNA) expression in LAD without lymphatic metastasis versus paired adjacent non‐tumor (ANT) lung tissues and LAD with versus without lymphatic metastasis were analyzed using Human LncRNA Arraystar V3.0.

    Techniques: Expressing

    Long non‐coding RNA (lncRNA) and messenger RNA (mRNA) differential expression characteristics. A scatter plot shows the differences between ( a ) lncRNA and ( b ) mRNA expression in lung adenocarcinoma (LAD) without lymphatic metastasis (group‐Exp1) versus adjacent non‐tumor (ANT) lung tissues (group‐ctrl). A scatter plot of the differences in ( c ) lncRNA and ( d ) mRNA expression in LAD with lymphatic metastasis (group‐Exp2) versus LAD without lymphatic metastasis (group‐Exp1). The relative expression level increases from blue to red (≥ 2‐fold, P

    Journal: Thoracic Cancer

    Article Title: Microarray expression profile of long non‐coding RNAs in human lung adenocarcinoma

    doi: 10.1111/1759-7714.12845

    Figure Lengend Snippet: Long non‐coding RNA (lncRNA) and messenger RNA (mRNA) differential expression characteristics. A scatter plot shows the differences between ( a ) lncRNA and ( b ) mRNA expression in lung adenocarcinoma (LAD) without lymphatic metastasis (group‐Exp1) versus adjacent non‐tumor (ANT) lung tissues (group‐ctrl). A scatter plot of the differences in ( c ) lncRNA and ( d ) mRNA expression in LAD with lymphatic metastasis (group‐Exp2) versus LAD without lymphatic metastasis (group‐Exp1). The relative expression level increases from blue to red (≥ 2‐fold, P

    Article Snippet: LncRNA and messenger RNA (mRNA) expression in LAD without lymphatic metastasis versus paired adjacent non‐tumor (ANT) lung tissues and LAD with versus without lymphatic metastasis were analyzed using Human LncRNA Arraystar V3.0.

    Techniques: Expressing

    Renin and Collagen I Messenger RNA Expression

    Journal: Transplantation

    Article Title: Calcineurin-inhibition Results in Upregulation of Local Renin and Subsequent Vascular Endothelial Growth Factor Production in Renal Collecting Ducts

    doi: 10.1097/TP.0000000000000961

    Figure Lengend Snippet: Renin and Collagen I Messenger RNA Expression

    Article Snippet: The messenger RNA (mRNA) expression of renin, collagen I, and glyceraldehyde-3-phosphate dehydrogenase were determined on a Light Cycler 480 system (Roche Diagnostics, Mannheim, Germany).

    Techniques: RNA Expression

    Gene expression of mitochondrial targets measured by RT-PCR. mRNA expression UCP2 was increased in offspring of protein-restricted dams. ATP Synthetase β -subunit and ATP-ADP translocase 1 were unaffected by maternal protein restriction. Values are means ± S.E.M. n = 5 animals per group.* P

    Journal: Journal of Nutrition and Metabolism

    Article Title: Mitochondrial Respiration Is Decreased in Rat Kidney Following Fetal Exposure to a MaternalLow-ProteinDiet

    doi: 10.1155/2012/989037

    Figure Lengend Snippet: Gene expression of mitochondrial targets measured by RT-PCR. mRNA expression UCP2 was increased in offspring of protein-restricted dams. ATP Synthetase β -subunit and ATP-ADP translocase 1 were unaffected by maternal protein restriction. Values are means ± S.E.M. n = 5 animals per group.* P

    Article Snippet: To assess this as a potential target for nutritional programming, we determined the mRNA expression of ATP synthetase and ATP-ADP translocase 1, which is one of the proteins responsible for movement of ATP and ADP across the innermitochondrial membrane.

    Techniques: Expressing, Reverse Transcription Polymerase Chain Reaction

    Messenger ribonucleic acid (mRNA) expression of hypoxia-inducible factor (HIF)-1α, p67-phox, senescence marker protein-30 (SMP30), connective tissue growth factor (CTGF), monocyte chemotactic protein-1 (MCP-1) and peroxisome proliferator-activated receptor-gamma coactivator-1α (PGC-1α). Relative expression of HIF-1 α, p67-phox , SMP30 , CTGF , MCP-1 and PGC-1 α in whole kidney were determined by reverse transcription polymerase chain reaction. mRNA content of wild-type (WT) control (Cont) mice was designated as 1.0. Values are means ± standard error; † P

    Journal: Journal of Diabetes Investigation

    Article Title: Senescence marker protein-30/gluconolactonase deficiency exacerbates diabetic nephropathy through tubular injury in a mouse model of type 1 diabetes

    doi: 10.1111/jdi.12252

    Figure Lengend Snippet: Messenger ribonucleic acid (mRNA) expression of hypoxia-inducible factor (HIF)-1α, p67-phox, senescence marker protein-30 (SMP30), connective tissue growth factor (CTGF), monocyte chemotactic protein-1 (MCP-1) and peroxisome proliferator-activated receptor-gamma coactivator-1α (PGC-1α). Relative expression of HIF-1 α, p67-phox , SMP30 , CTGF , MCP-1 and PGC-1 α in whole kidney were determined by reverse transcription polymerase chain reaction. mRNA content of wild-type (WT) control (Cont) mice was designated as 1.0. Values are means ± standard error; † P

    Article Snippet: Reverse transcription polymerase chain reaction was used to measure messenger RNA (mRNA) expression of HIF-1α, p67-phox, SMP30, connective tissue growth factor (CTGF), monocyte chemotactic protein-1 (MCP-1) and peroxisome proliferator-activated receptor-gamma coactivator-1α (PGC-1α) using a Thermal Cycler Dice Real Time System II (TaKaRa Bio Inc.).

    Techniques: Expressing, Marker, Pyrolysis Gas Chromatography, Reverse Transcription Polymerase Chain Reaction, Mouse Assay

    mRNA expression of RFC in 39 human biopsy samples relative to the calibrator (A–E). Solid horizontal lines demonstrate the median of each individual group. All data are shown as the ratio between the target gene and beta-actin. * P -value, non-parametric, Mann-Whitney or Kruskal-Wallis tests. BA, Bilharizal-associated.

    Journal: PLoS ONE

    Article Title: Expression of RFC/SLC19A1 is Associated with Tumor Type in Bladder Cancer Patients

    doi: 10.1371/journal.pone.0021820

    Figure Lengend Snippet: mRNA expression of RFC in 39 human biopsy samples relative to the calibrator (A–E). Solid horizontal lines demonstrate the median of each individual group. All data are shown as the ratio between the target gene and beta-actin. * P -value, non-parametric, Mann-Whitney or Kruskal-Wallis tests. BA, Bilharizal-associated.

    Article Snippet: mRNA expression of RFC The mRNA expression of the folate transporter RFC was quantified in 41 bladder cancer specimens, three specimens with no evidence of malignancy obtained from bladder mucosa adjacent to cancerous tissue, and a commercially available reference bladder RNA pooled from 26 male/female Caucasians; aged 22–70 (Clonetech, Germany).

    Techniques: Expressing, MANN-WHITNEY

    Effects of ROCK1 and ZIPK knockdown on IL-6 and IL-1β mRNA expression and IL-6 protein secretion. (A) CASMCs were transfected with siRNA to ZIPK or ROCK1 or with negative control siRNA. Cells were lysed 48 h later for qRT-PCR to quantify IL-6 and IL-1β mRNA levels. Values represent means ± SEM ( n = 7 for IL-6 and n = 6 for IL-1β). *significantly different from control (p

    Journal: PLoS ONE

    Article Title: The Effects of Knockdown of Rho-Associated Kinase 1 and Zipper-Interacting Protein Kinase on Gene Expression and Function in Cultured Human Arterial Smooth Muscle Cells

    doi: 10.1371/journal.pone.0116969

    Figure Lengend Snippet: Effects of ROCK1 and ZIPK knockdown on IL-6 and IL-1β mRNA expression and IL-6 protein secretion. (A) CASMCs were transfected with siRNA to ZIPK or ROCK1 or with negative control siRNA. Cells were lysed 48 h later for qRT-PCR to quantify IL-6 and IL-1β mRNA levels. Values represent means ± SEM ( n = 7 for IL-6 and n = 6 for IL-1β). *significantly different from control (p

    Article Snippet: Levels of mRNA expression were quantified by RT-PCR using a BioRad iCycler MyiQ detection system (BioRad) with pre-synthesized primers (Applied Biosystems) for ZIPK (Hs00154676_m1), IL-1β (Hs00174097_m1) and IL-6 (Hs00174131_m1).

    Techniques: Expressing, Transfection, Negative Control, Quantitative RT-PCR

    mRNA expression of aggrecan and collagen-I in ADMSCs under the IVD-like chemical conditions . RT-PCR analysis of aggrecan and collagen-I mRNA levels in ADMSCs cultured for 1 week or 2 weeks under IVD-like chemical conditions. Statistically significant differences were indicated with asterisks, * P

    Journal: Journal of Translational Medicine

    Article Title: Responses of human adipose-derived mesenchymal stem cells to chemical microenvironment of the intervertebral disc

    doi: 10.1186/1479-5876-10-49

    Figure Lengend Snippet: mRNA expression of aggrecan and collagen-I in ADMSCs under the IVD-like chemical conditions . RT-PCR analysis of aggrecan and collagen-I mRNA levels in ADMSCs cultured for 1 week or 2 weeks under IVD-like chemical conditions. Statistically significant differences were indicated with asterisks, * P

    Article Snippet: The quantification of mRNA expression levels for aggrecan and collagen-I were carried out on an iCycler system (Bio-Rad, Laboratories, Hercules, CA, USA). iQ™SYBR Green super mix PCR kit (Bio-Rad) was used for real-time monitoring of amplification (5 ng of template cDNA; 45 cycles: 95°C/10 s, 62°C/25 s) with appropriate primers (Table 2).

    Techniques: Expressing, Reverse Transcription Polymerase Chain Reaction, Cell Culture

    ADORA2A methylation and A2aR mRNA expression in leucocyte subtypes. A) Mean methylation of CD8 + T, CD4 + T, Treg, B cells, and monocytes as well as HPV-positive and HPV-negative cell lines at different loci within ADORA2A targeted by beads from the Infinium HumanMethylation450 BeadChip. B) A2aR mRNA expression in monocytes, B, CD4 + , and CD8 + T cells. Asteriks imply a significant difference between two groups (*: p°

    Journal: Oncoimmunology

    Article Title: Detailed analysis of adenosine A2a receptor (ADORA2A) and CD73 (5′-nucleotidase, ecto, NT5E) methylation and gene expression in head and neck squamous cell carcinoma patients

    doi: 10.1080/2162402X.2018.1452579

    Figure Lengend Snippet: ADORA2A methylation and A2aR mRNA expression in leucocyte subtypes. A) Mean methylation of CD8 + T, CD4 + T, Treg, B cells, and monocytes as well as HPV-positive and HPV-negative cell lines at different loci within ADORA2A targeted by beads from the Infinium HumanMethylation450 BeadChip. B) A2aR mRNA expression in monocytes, B, CD4 + , and CD8 + T cells. Asteriks imply a significant difference between two groups (*: p°

    Article Snippet: Methylation and mRNA expression were generated by the Infinium HumanMethylation450 BeadChip and Illumina HiSeq 2000 RNA Sequencing Version 2 analysis (Illumina, Inc., San Diego, CA, USA).

    Techniques: Methylation, Expressing

    Messenger RNA expression analysis of matched fresh and FFPE RNA using different RNA extraction methods. The upper panel displays a graphic representation of quantitative RT-PCR (Taqman® mRNA assays) Measurements obtained for ESR1, CCND2 and KRT14 genes using matched fresh and FFPE RNA from MCF10A cells. The three genes were quantified using matched fresh RNA recovered with TRIzol (TRI-Fr), and FFPE RNA recovered with TRIzol (TRI), with Qiagen AllPrep DNA/RNA FFPE (QDR), with AMBion RecoverAll™ Total Nucleic Acid Isolation (AMB) and with the Roche RNA FFPE (Roche) kits. The results are represented as fold changes. The lower panels show the comparison of global mRNA quantifications obtained between fresh and FFPE RNA samples using the Illumina whole-Genome DASL platform. The different panels display comparison between triplicate RNA extractions from matched fresh (TRI-Fr1, TRI-Fr2, TRI-Fr3 (bottom to top panel)) and FFPE (TRI1-3, QDR1-3, AMB1-3 and Roche1-3 (from left to right panel)) cells. The correlation coefficient (r) between matched fresh and FFPE RNAs is displayed in each graph.

    Journal: PLoS ONE

    Article Title: Effective DNA/RNA Co-Extraction for Analysis of MicroRNAs, mRNAs, and Genomic DNA from Formalin-Fixed Paraffin-Embedded Specimens

    doi: 10.1371/journal.pone.0034683

    Figure Lengend Snippet: Messenger RNA expression analysis of matched fresh and FFPE RNA using different RNA extraction methods. The upper panel displays a graphic representation of quantitative RT-PCR (Taqman® mRNA assays) Measurements obtained for ESR1, CCND2 and KRT14 genes using matched fresh and FFPE RNA from MCF10A cells. The three genes were quantified using matched fresh RNA recovered with TRIzol (TRI-Fr), and FFPE RNA recovered with TRIzol (TRI), with Qiagen AllPrep DNA/RNA FFPE (QDR), with AMBion RecoverAll™ Total Nucleic Acid Isolation (AMB) and with the Roche RNA FFPE (Roche) kits. The results are represented as fold changes. The lower panels show the comparison of global mRNA quantifications obtained between fresh and FFPE RNA samples using the Illumina whole-Genome DASL platform. The different panels display comparison between triplicate RNA extractions from matched fresh (TRI-Fr1, TRI-Fr2, TRI-Fr3 (bottom to top panel)) and FFPE (TRI1-3, QDR1-3, AMB1-3 and Roche1-3 (from left to right panel)) cells. The correlation coefficient (r) between matched fresh and FFPE RNAs is displayed in each graph.

    Article Snippet: Messenger RNA Expression Profiling mRNA expression profiling (24,526 features) was performed with total RNA extracted from fresh and FFPE cells (200 ng) using the Illumina Whole genome c D NA-mediated A nnealing, S election, Extension and L igation (DASL) assay on 32 beadchip arrays, following manufacturer's instructions and according to Loudig et al. 2011 .

    Techniques: RNA Expression, Formalin-fixed Paraffin-Embedded, RNA Extraction, Quantitative RT-PCR, Isolation

    Flow figure indicating study design Step I: We identified and analyzed DMGs through TCGA methylation profiles. By using Pearson Correlation Coefficient method, we got the CpG sites which may influence gene expression. Then gene ontology (GO) functional analysis and KEGG subpathway enrichment analysis were performed for the DMGs. Step II: We identified and analyzed DEGs through mRNA expression profiles. GO functional analysis and KEGG subpathway enrichment analysis were performed for DEGs using the same method mentioned above. Step III: Based on topological property analysis of the integrated network, we identified candidate genes associated with the survival of KIRC both in the training set and testing set.

    Journal: Oncotarget

    Article Title: Identifying prognostic biomarkers based on aberrant DNA methylation in kidney renal clear cell carcinoma

    doi: 10.18632/oncotarget.14134

    Figure Lengend Snippet: Flow figure indicating study design Step I: We identified and analyzed DMGs through TCGA methylation profiles. By using Pearson Correlation Coefficient method, we got the CpG sites which may influence gene expression. Then gene ontology (GO) functional analysis and KEGG subpathway enrichment analysis were performed for the DMGs. Step II: We identified and analyzed DEGs through mRNA expression profiles. GO functional analysis and KEGG subpathway enrichment analysis were performed for DEGs using the same method mentioned above. Step III: Based on topological property analysis of the integrated network, we identified candidate genes associated with the survival of KIRC both in the training set and testing set.

    Article Snippet: Two sets of paired data (cancerous and normal adjacent tissues from KIRC patients) were downloaded, including mRNA expression profiles (level 3 data, RNA-seq Version 2, Illumina) of 532 cancer samples and 71 adjacent tissues from KIRC patients; the gene set type is Refseq, DNA methylation profiles (level 3 data, Infinium HumanMethylation450BeadChIP) of 321 cancer samples and 158 adjacent tissues from KIRC patients.

    Techniques: Flow Cytometry, Methylation, Expressing, Functional Assay

    miRNA–mRNA regulatory networks in different human diseases. ( A ) Type 2 diabetes miRNA–mRNA network: The network consisted of 80 nodes, comprising five differentially expressed (DE) miRNAs and 75 DE mRNA targets, with 78 edges showing the

    Journal: RNA

    Article Title: MicroRNAs act complementarily to regulate disease-related mRNA modules in human diseases

    doi: 10.1261/rna.038414.113

    Figure Lengend Snippet: miRNA–mRNA regulatory networks in different human diseases. ( A ) Type 2 diabetes miRNA–mRNA network: The network consisted of 80 nodes, comprising five differentially expressed (DE) miRNAs and 75 DE mRNA targets, with 78 edges showing the

    Article Snippet: We performed miRNA- and mRNA-expression profiling using Illumina's Human v2 miRNA panel and HumanWG-6 v3.0 Expression BeadChips (Illumina), respectively, on the allergen- and diluent-challenged samples derived from all the 40 subjects, according to the manufacturer's instructions.

    Techniques:

    The mRNA expression of IL - 17A with the mRNA expression of IL - 4 , cytokine IL-4 and SCS values among different genotypes in Sanhe Cattle. a Relative mRNA expression of 3 genotypes of SNP in IL - 17A gene. b Relative mRNA expression of 3 genotypes of SNP in IL - 17A in association with IL-4 gene. c Comparison of the genotypes with respect to SCS. d Comparison of the 3 genotypes with respect to the IL-4 cytokines

    Journal: Journal of Animal Science and Biotechnology

    Article Title: Novel SNPs in IL-17F and IL-17A genes associated with somatic cell count in Chinese Holstein and Inner-Mongolia Sanhe cattle

    doi: 10.1186/s40104-016-0137-1

    Figure Lengend Snippet: The mRNA expression of IL - 17A with the mRNA expression of IL - 4 , cytokine IL-4 and SCS values among different genotypes in Sanhe Cattle. a Relative mRNA expression of 3 genotypes of SNP in IL - 17A gene. b Relative mRNA expression of 3 genotypes of SNP in IL - 17A in association with IL-4 gene. c Comparison of the genotypes with respect to SCS. d Comparison of the 3 genotypes with respect to the IL-4 cytokines

    Article Snippet: In order to display the trends of mRNA expression of different genotypes of IL -17A gene with the mRNA expression of IL -4 gene, cytokine IL-4 and SCS values, we draw a line chart as shown in Fig. .

    Techniques: Expressing

    The trends of mRNA expression of different genotypes of IL - 17A gene in Sanhe Cattle. a Trends of mRNA expression of different genotypes of IL - 17A gene with IL - 4 gene. b Trends of mRNA expression of different genotypes of IL - 17A gene with IL-4 cytokine. c Trends of mRNA expression of different genotypes of IL - 17A gene with SCS values

    Journal: Journal of Animal Science and Biotechnology

    Article Title: Novel SNPs in IL-17F and IL-17A genes associated with somatic cell count in Chinese Holstein and Inner-Mongolia Sanhe cattle

    doi: 10.1186/s40104-016-0137-1

    Figure Lengend Snippet: The trends of mRNA expression of different genotypes of IL - 17A gene in Sanhe Cattle. a Trends of mRNA expression of different genotypes of IL - 17A gene with IL - 4 gene. b Trends of mRNA expression of different genotypes of IL - 17A gene with IL-4 cytokine. c Trends of mRNA expression of different genotypes of IL - 17A gene with SCS values

    Article Snippet: In order to display the trends of mRNA expression of different genotypes of IL -17A gene with the mRNA expression of IL -4 gene, cytokine IL-4 and SCS values, we draw a line chart as shown in Fig. .

    Techniques: Expressing

    Venn diagram of overlapping mRNA and lncRNA derived from three group comparisons. a Differentially expressed mRNAs are represented on this Venn diagram, showing either distinct or overlapping relationship with depression or resiliency phenotype. b The diagram represents the unique and overlapping phenotypic association of differentially expressed lncRNA with resiliency or susceptibility to develop depression

    Journal: Translational Psychiatry

    Article Title: Co-expression network modeling identifies key long non-coding RNA and mRNA modules in altering molecular phenotype to develop stress-induced depression in rats

    doi: 10.1038/s41398-019-0448-z

    Figure Lengend Snippet: Venn diagram of overlapping mRNA and lncRNA derived from three group comparisons. a Differentially expressed mRNAs are represented on this Venn diagram, showing either distinct or overlapping relationship with depression or resiliency phenotype. b The diagram represents the unique and overlapping phenotypic association of differentially expressed lncRNA with resiliency or susceptibility to develop depression

    Article Snippet: Transcriptome-wide lncRNA and mRNA expression was measured using one color high throughput microarray-based microarray protocol using Agilent microarray chip (4 × 44 K) which contained 13,611 lncRNAs and 24,626 mRNAs.

    Techniques: Derivative Assay

    3’UTR target analysis for methylation sensitive miRNA ( a ) Scatter plot of the number of miRNAs predicted to target the mRNA (Y axis) vs. the maximum inverse correlation exhibited between the mRNA the miRNAs (X axis). Labeled mRNAs from the top 5% are significantly associated with poor OS when over-expressed in tumors. ( b ) A radial bipartite graph showing mRNAs highlighted in (a) with miRNA interactions. Only genes with significant associations with OS are depicted. Edge thickness is proportional to both inverse expression correlation and the over-representation of predicted mRNA targets. ( c ) Gene ontology analysis for the 1,250 over-represented target mRNAs with significant inverse correlation to the 67 methylation sensitive miRNAs.(*p

    Journal: Oncogene

    Article Title: Modulation of Neuroblastoma Disease Pathogenesis By An Extensive Network of Epigenetically Regulated MicroRNAs

    doi: 10.1038/onc.2012.311

    Figure Lengend Snippet: 3’UTR target analysis for methylation sensitive miRNA ( a ) Scatter plot of the number of miRNAs predicted to target the mRNA (Y axis) vs. the maximum inverse correlation exhibited between the mRNA the miRNAs (X axis). Labeled mRNAs from the top 5% are significantly associated with poor OS when over-expressed in tumors. ( b ) A radial bipartite graph showing mRNAs highlighted in (a) with miRNA interactions. Only genes with significant associations with OS are depicted. Edge thickness is proportional to both inverse expression correlation and the over-representation of predicted mRNA targets. ( c ) Gene ontology analysis for the 1,250 over-represented target mRNAs with significant inverse correlation to the 67 methylation sensitive miRNAs.(*p

    Article Snippet: A subgroup of tumors was used for the methylation analysis ( ) and for integrated analysis of miRNA (TaqMan qPCR) and mRNA expression (Affymetrix Exon arrays).

    Techniques: Methylation, Labeling, Expressing

    Analysis of SOX2 as a miR-340 target ( a ) SOX2 mRNA levels assessed by TaqMan qPCR three days post-transfection of SK-N-BE cells with miR-340. ( b ) SOX2 mRNA levels in cells treated and untreated with ATRA for 7 days ( c ) SOX2 protein levels in miR-340 transfected SK-N-BE cells and in cells treated with ATRA. ( d ) Three distinct miR-340 target sites within the 1.1 kb 3’-UTR of SOX2 (TargetScan). The sites are designated 1910, 2137 and 2192 based upon the position of the first nucleotide of the seed site in the numbering of GenBank sequence NM_003106.3. ( e ) A panel of luciferase reporter plasmids with wild type and mutant target sites within the SOX2 3’ UTR. psi-SOX2-3’ UTR has the entire wild type 3’UTR; psi-SOX2-TRM is a triple deletion mutant for all three seed sites; double mutants are designated by the single site remaining active (e.g. psi-SOX2-1910 has the 2137 and 2192 seed regions deleted); and single mutants are designated by the two sites remaining active (e.g. psi-SOX2-2137-2192 has the 1910 seed site deleted). The bar graph demonstrates the effects on luciferase activity 48 hours after co-transfection of each construct with either miR-340 or a negative control. Renilla luciferase activity was normalized to fire fly luciferase (*p

    Journal: Oncogene

    Article Title: Modulation of Neuroblastoma Disease Pathogenesis By An Extensive Network of Epigenetically Regulated MicroRNAs

    doi: 10.1038/onc.2012.311

    Figure Lengend Snippet: Analysis of SOX2 as a miR-340 target ( a ) SOX2 mRNA levels assessed by TaqMan qPCR three days post-transfection of SK-N-BE cells with miR-340. ( b ) SOX2 mRNA levels in cells treated and untreated with ATRA for 7 days ( c ) SOX2 protein levels in miR-340 transfected SK-N-BE cells and in cells treated with ATRA. ( d ) Three distinct miR-340 target sites within the 1.1 kb 3’-UTR of SOX2 (TargetScan). The sites are designated 1910, 2137 and 2192 based upon the position of the first nucleotide of the seed site in the numbering of GenBank sequence NM_003106.3. ( e ) A panel of luciferase reporter plasmids with wild type and mutant target sites within the SOX2 3’ UTR. psi-SOX2-3’ UTR has the entire wild type 3’UTR; psi-SOX2-TRM is a triple deletion mutant for all three seed sites; double mutants are designated by the single site remaining active (e.g. psi-SOX2-1910 has the 2137 and 2192 seed regions deleted); and single mutants are designated by the two sites remaining active (e.g. psi-SOX2-2137-2192 has the 1910 seed site deleted). The bar graph demonstrates the effects on luciferase activity 48 hours after co-transfection of each construct with either miR-340 or a negative control. Renilla luciferase activity was normalized to fire fly luciferase (*p

    Article Snippet: A subgroup of tumors was used for the methylation analysis ( ) and for integrated analysis of miRNA (TaqMan qPCR) and mRNA expression (Affymetrix Exon arrays).

    Techniques: Real-time Polymerase Chain Reaction, Transfection, Sequencing, Luciferase, Mutagenesis, Activity Assay, Cotransfection, Construct, Negative Control

    Analysis of IL-6 mRNA levels within synovial tissue from rheumatoid arthritis (RA) as compared with that from osteoarthritis (OA) patients. Upper panels: quality control of total RNA preparations. Aliquots (300 ng) of total RNA extracted from synovial tissue from RA and OA patients were plotted on a RNA 6000 Nano-LabChip. Quality of RNA was scanned using a 2100 bioanalyzer. RNA gel electropherograms show the presence of 28S and 18S ribosomal units, indicating intact RNA of the investigated samples. Lower panels: differential IL-6 mRNA levels were determined by semiquantitative reverse transcription polymerase chain reaction (PCR). The figure shows a representative analysis of eight cDNA samples derived from patients with RA and of eight cDNA samples from patients with OA. cDNA samples were adjusted to equal glyceraldehyde-3-phosphate dehydrogenase (G3PDH) levels, performed by competitive PCR using an internal standard (see Materials and methods). Numbered lanes correspond to individual patients within Table 1 .

    Journal: Arthritis Research & Therapy

    Article Title: High CXCR3 expression in synovial mast cells associated with CXCL9 and CXCL10 expression in inflammatory synovial tissues of patients with rheumatoid arthritis

    doi:

    Figure Lengend Snippet: Analysis of IL-6 mRNA levels within synovial tissue from rheumatoid arthritis (RA) as compared with that from osteoarthritis (OA) patients. Upper panels: quality control of total RNA preparations. Aliquots (300 ng) of total RNA extracted from synovial tissue from RA and OA patients were plotted on a RNA 6000 Nano-LabChip. Quality of RNA was scanned using a 2100 bioanalyzer. RNA gel electropherograms show the presence of 28S and 18S ribosomal units, indicating intact RNA of the investigated samples. Lower panels: differential IL-6 mRNA levels were determined by semiquantitative reverse transcription polymerase chain reaction (PCR). The figure shows a representative analysis of eight cDNA samples derived from patients with RA and of eight cDNA samples from patients with OA. cDNA samples were adjusted to equal glyceraldehyde-3-phosphate dehydrogenase (G3PDH) levels, performed by competitive PCR using an internal standard (see Materials and methods). Numbered lanes correspond to individual patients within Table 1 .

    Article Snippet: Because pooled samples may sometimes produce obscure findings and PCR-based methods are known to be more sensitive than the Affymetrix gene chip technology, semiquantitative RT-PCR was introduced to validate Affymetrix-derived mRNA expression levels in individual patient samples (RA, n = 20; OA, n = 10).

    Techniques: Reverse Transcription Polymerase Chain Reaction, Polymerase Chain Reaction, Derivative Assay

    Changes in mRNA expression of proliferation- (A) and apoptosis-regulating genes (B) during aging (Children /Ch/ vs. Healthy adult /N/ colonic epithelium) and carcinogenesis (Healthy adult /N/ vs. Colorectal cancer /CRC/) using Affymetrix HGU133 Plus2.0 array. On the heat map, increased gene expression is represented with red lines, while decreased expression with green. The first 6 samples with light blue show genes in children, the dark blue are from healthy adults, while the last samples in green are from cancer patients.

    Journal: PLoS ONE

    Article Title: Sporadic Colorectal Cancer Development Shows Rejuvenescence Regarding Epithelial Proliferation and Apoptosis

    doi: 10.1371/journal.pone.0074140

    Figure Lengend Snippet: Changes in mRNA expression of proliferation- (A) and apoptosis-regulating genes (B) during aging (Children /Ch/ vs. Healthy adult /N/ colonic epithelium) and carcinogenesis (Healthy adult /N/ vs. Colorectal cancer /CRC/) using Affymetrix HGU133 Plus2.0 array. On the heat map, increased gene expression is represented with red lines, while decreased expression with green. The first 6 samples with light blue show genes in children, the dark blue are from healthy adults, while the last samples in green are from cancer patients.

    Article Snippet: For mRNA expression profiles the Affymetrix expression arrays were primarily pre-processed by GCRMA background correction method with quantile normalization and median polish summarization.

    Techniques: Expressing

    Upregulation of miR-218 reduces Robo1 expression through the inactivation of Slit2-Robo1 signaling. (A and B) The U87 cells were treated with control, NC and miR-218 mimics, and the levels of Robo1 and Slit2 mRNA were measured by quantitative polymerase chain reaction.(C) The level of Robo1 and Slit2 protein expression in the U87 cells was measured by western blot analysis. * P

    Journal: Oncology Letters

    Article Title: miR-218 inhibits the migration and invasion of glioma U87 cells through the Slit2-Robo1 pathway

    doi: 10.3892/ol.2015.2904

    Figure Lengend Snippet: Upregulation of miR-218 reduces Robo1 expression through the inactivation of Slit2-Robo1 signaling. (A and B) The U87 cells were treated with control, NC and miR-218 mimics, and the levels of Robo1 and Slit2 mRNA were measured by quantitative polymerase chain reaction.(C) The level of Robo1 and Slit2 protein expression in the U87 cells was measured by western blot analysis. * P

    Article Snippet: The mRNA expression of Slit2 and Robo1 was analyzed by qPCR, using the SYBR-Green method.

    Techniques: Expressing, Real-time Polymerase Chain Reaction, Western Blot

    Effects of SLIT2 expression on biomarker gene expression and GC proliferation. ( A ) The granulosa cells were transfected with the reconstructed pYr-adshuttle-4-SLIT2 plasmids, a pYr-adshuttle-4 empty vector (negative control) or no plasmid (blank control). The expression of the biomarker genes FSHR , GDF9, STAR and CYP11A1 before and after the GCs were transfected with the pYr-adshuttle-4-SLIT2 expression vector for 24 h was examined by qRT-PCR. The mRNA expression was normalized to that of the 18S rRNA gene; the values on the bar graphs represent the mean ± SEM of 10 hens (n = 10) from a representative experiment. ( B ) GC proliferation was detected by an EdU incorporation assay. ( C ) The GCs were transfected with SLIT2 specific siRNAs, scrambled siRNA (negative control) or no siRNA (blank control). The expression of the biomarker genes in GCs transfected with or without the specific siRNA was examined by qRT-PCR. The mRNA expression was normalized to that of the 18S rRNA gene; the values on the bar graphs represent the mean ± SEM of 10 hens. ( D ) GC proliferation was detected by an EdU incorporation assay. For each group, the superscript symbol above the bar indicates that the difference was significant compared to the control group **P

    Journal: Scientific Reports

    Article Title: Inhibitory effect of SLIT2 on granulosa cell proliferation mediated by the CDC42-PAKs-ERK1/2 MAPK pathway in the prehierarchical follicles of the chicken ovary

    doi: 10.1038/s41598-018-27601-z

    Figure Lengend Snippet: Effects of SLIT2 expression on biomarker gene expression and GC proliferation. ( A ) The granulosa cells were transfected with the reconstructed pYr-adshuttle-4-SLIT2 plasmids, a pYr-adshuttle-4 empty vector (negative control) or no plasmid (blank control). The expression of the biomarker genes FSHR , GDF9, STAR and CYP11A1 before and after the GCs were transfected with the pYr-adshuttle-4-SLIT2 expression vector for 24 h was examined by qRT-PCR. The mRNA expression was normalized to that of the 18S rRNA gene; the values on the bar graphs represent the mean ± SEM of 10 hens (n = 10) from a representative experiment. ( B ) GC proliferation was detected by an EdU incorporation assay. ( C ) The GCs were transfected with SLIT2 specific siRNAs, scrambled siRNA (negative control) or no siRNA (blank control). The expression of the biomarker genes in GCs transfected with or without the specific siRNA was examined by qRT-PCR. The mRNA expression was normalized to that of the 18S rRNA gene; the values on the bar graphs represent the mean ± SEM of 10 hens. ( D ) GC proliferation was detected by an EdU incorporation assay. For each group, the superscript symbol above the bar indicates that the difference was significant compared to the control group **P

    Article Snippet: As shown in Fig. , the mRNA expression levels of FSHR, GDF9 , STAR and CYP11A1 were significantly down-regulated in the cells with the SLIT2 overexpression (P < 0.01), and the cell proliferation ratios of the GCs were markedly decreased compared with those in the negative control (P < 0.01) (Fig. , Supplemental Fig. ).

    Techniques: Expressing, Biomarker Assay, Transfection, Plasmid Preparation, Negative Control, Quantitative RT-PCR

    Schematic representation of the role of SLIT2-ROBO1/ROBO2 in the regulation of ovarian prehierarchical follicle growth and development mediated by the CDC42-RAFs-ERK1/2 MAPK cascade in hens. ( 1 ) The SLIT2 ligand interacts with ROBO1 and/or ROBO2 in an autocrine or paracrine manner and activates its downstream mediator SRGAP1 of SLIT/ROBO signaling. ( 2 ) Following the stimulation of the activated SRGAP1, the expression level of the activated endogenous GTP-binding CDC42 protein is down-regulated to enhance the intrinsic GTPase activity of CDC42 by stimulating GTP hydrolysis. Then, the activity levels of its downstream PAK effectors are attenuated, finally leading to the inhibitory effects of the MAPK/ERK signaling pathway on cell proliferation, differentiation and follicle selection. ( 3 ) The inhibitory effect of SLIT2-ROBO1/2 on GC proliferation, differentiation and follicle selection may be mainly mediated by CDC42/PAK1 via the MAPK/ERK1/2 signaling cascade and partially mediated by PAK2 and PAK3. ( 4 ) The effect of the inhibition of ERK1/2 induced by the interaction between SLIT2 and ROBO1/2 on the transcription of FSHR , GDF9, STAR and CYP11A1 mRNA in the nucleus. ( 5 ) The reduced transcript and protein expression levels of FSHR may decrease the capacity of the FSHR to response to FSH. FSH-induced cell signaling via the protein kinase A/cyclic adenosine monophosphate (cAMP) pathway has been shown to be required for initiating differentiation in granulosa cells during follicle selection 5 , 7 , 9 , 49 .

    Journal: Scientific Reports

    Article Title: Inhibitory effect of SLIT2 on granulosa cell proliferation mediated by the CDC42-PAKs-ERK1/2 MAPK pathway in the prehierarchical follicles of the chicken ovary

    doi: 10.1038/s41598-018-27601-z

    Figure Lengend Snippet: Schematic representation of the role of SLIT2-ROBO1/ROBO2 in the regulation of ovarian prehierarchical follicle growth and development mediated by the CDC42-RAFs-ERK1/2 MAPK cascade in hens. ( 1 ) The SLIT2 ligand interacts with ROBO1 and/or ROBO2 in an autocrine or paracrine manner and activates its downstream mediator SRGAP1 of SLIT/ROBO signaling. ( 2 ) Following the stimulation of the activated SRGAP1, the expression level of the activated endogenous GTP-binding CDC42 protein is down-regulated to enhance the intrinsic GTPase activity of CDC42 by stimulating GTP hydrolysis. Then, the activity levels of its downstream PAK effectors are attenuated, finally leading to the inhibitory effects of the MAPK/ERK signaling pathway on cell proliferation, differentiation and follicle selection. ( 3 ) The inhibitory effect of SLIT2-ROBO1/2 on GC proliferation, differentiation and follicle selection may be mainly mediated by CDC42/PAK1 via the MAPK/ERK1/2 signaling cascade and partially mediated by PAK2 and PAK3. ( 4 ) The effect of the inhibition of ERK1/2 induced by the interaction between SLIT2 and ROBO1/2 on the transcription of FSHR , GDF9, STAR and CYP11A1 mRNA in the nucleus. ( 5 ) The reduced transcript and protein expression levels of FSHR may decrease the capacity of the FSHR to response to FSH. FSH-induced cell signaling via the protein kinase A/cyclic adenosine monophosphate (cAMP) pathway has been shown to be required for initiating differentiation in granulosa cells during follicle selection 5 , 7 , 9 , 49 .

    Article Snippet: As shown in Fig. , the mRNA expression levels of FSHR, GDF9 , STAR and CYP11A1 were significantly down-regulated in the cells with the SLIT2 overexpression (P < 0.01), and the cell proliferation ratios of the GCs were markedly decreased compared with those in the negative control (P < 0.01) (Fig. , Supplemental Fig. ).

    Techniques: Expressing, Binding Assay, Activity Assay, Selection, Inhibition

    Effects of ROBO1/2 interference on biomarker gene expression and GC proliferation. In the GCs transfected with or without the reconstructed pYr-adshuttle-4-SLIT2 plasmids, the cells were co-transfected with specific siRNAs targeting the ROBO1 and/or ROBO2 genes. GC proliferation was examined by an EdU incorporation assay (original magnification × 20). ( A ) The effect of the ROBO1 interference on granulosa cell proliferation. ( B ) The effect of the ROBO2 interference on granulosa cell proliferation. ( C ) The effect of the ROBO1 and ROBO2 co-interference on granulosa cell proliferation. ( D ) The effect of the ROBO1 and ROBO2 co-interference on the mRNA expression levels of the biomarker genes FSHR , GDF9, STAR and CYP11A1 . For each group, the different superscript above the bar indicates that the difference was significant (P

    Journal: Scientific Reports

    Article Title: Inhibitory effect of SLIT2 on granulosa cell proliferation mediated by the CDC42-PAKs-ERK1/2 MAPK pathway in the prehierarchical follicles of the chicken ovary

    doi: 10.1038/s41598-018-27601-z

    Figure Lengend Snippet: Effects of ROBO1/2 interference on biomarker gene expression and GC proliferation. In the GCs transfected with or without the reconstructed pYr-adshuttle-4-SLIT2 plasmids, the cells were co-transfected with specific siRNAs targeting the ROBO1 and/or ROBO2 genes. GC proliferation was examined by an EdU incorporation assay (original magnification × 20). ( A ) The effect of the ROBO1 interference on granulosa cell proliferation. ( B ) The effect of the ROBO2 interference on granulosa cell proliferation. ( C ) The effect of the ROBO1 and ROBO2 co-interference on granulosa cell proliferation. ( D ) The effect of the ROBO1 and ROBO2 co-interference on the mRNA expression levels of the biomarker genes FSHR , GDF9, STAR and CYP11A1 . For each group, the different superscript above the bar indicates that the difference was significant (P

    Article Snippet: As shown in Fig. , the mRNA expression levels of FSHR, GDF9 , STAR and CYP11A1 were significantly down-regulated in the cells with the SLIT2 overexpression (P < 0.01), and the cell proliferation ratios of the GCs were markedly decreased compared with those in the negative control (P < 0.01) (Fig. , Supplemental Fig. ).

    Techniques: Biomarker Assay, Expressing, Transfection

    Genetic alteration and gene expression of NOX family in GC. Notes: ( A ) Alteration frequency analysis of NOX genes in GC using cBioPortal. ( B ) Relative expression differences of NOX family genes in GC using Human Protein Atlas database. ( C ) Comparison of NOX1, NOX2, NOX4, NOX5, DUOX1, DUOX2 mRNA expression in gastric normal (left plot n=80) and cancer tissue (right plot n=80) in Cui dataset using Oncomine. Abbreviations: GC, gastric cancer; NADPH, nicotinamide adenine dinucleotide phosphate; NOX, NADPH oxidases.

    Journal: OncoTargets and therapy

    Article Title: Gene expression and prognosis of NOX family members in gastric cancer

    doi: 10.2147/OTT.S161287

    Figure Lengend Snippet: Genetic alteration and gene expression of NOX family in GC. Notes: ( A ) Alteration frequency analysis of NOX genes in GC using cBioPortal. ( B ) Relative expression differences of NOX family genes in GC using Human Protein Atlas database. ( C ) Comparison of NOX1, NOX2, NOX4, NOX5, DUOX1, DUOX2 mRNA expression in gastric normal (left plot n=80) and cancer tissue (right plot n=80) in Cui dataset using Oncomine. Abbreviations: GC, gastric cancer; NADPH, nicotinamide adenine dinucleotide phosphate; NOX, NADPH oxidases.

    Article Snippet: We investigated genetic alteration and mRNA expression of NOX family in GC patients via the cBioPortal, Human Protein Atlas, and Oncomine databases.

    Techniques: Expressing

    Active β-catenin, Prickle1 and Vangl2 are differently expressed in neuroblastoma cell lines. a Protein expression of active, de-phoshorylated β-catenin, the canonical Wnt/β-catenin target gene Axin2 and b . total β-catenin in neuroblastoma cell lines. SK-N-BE (2), SK-N-DZ, IMR-32 and Kelly are MYCN amplified neuroblastoma cells with high MycN expression. SH-SY5Y, SK-N-SH and SK-N-FI are non- MYCN amplified neuroblastoma cells expressing relatively low levels of MycN whereas, SK-N-AS and SHEP-1 do not show any MycN expression [ 33 ] c . Quantified protein expression (adjusted to β-actin) of Prickle1 and Vangl2 in neuroblastoma cell lines. Proteins were determined with western blotting. d mRNA expression in neuroblastoma cell lines SK-N-BE (2), SK-N-DZ, SK-N-AS, SH-EP1 and SH-SY5Y, assessed by quantitative real-time PCR, the data displayed is the mean ± S.D. of three determinations

    Journal: BMC Cancer

    Article Title: Planar cell polarity gene expression correlates with tumor cell viability and prognostic outcome in neuroblastoma

    doi: 10.1186/s12885-016-2293-2

    Figure Lengend Snippet: Active β-catenin, Prickle1 and Vangl2 are differently expressed in neuroblastoma cell lines. a Protein expression of active, de-phoshorylated β-catenin, the canonical Wnt/β-catenin target gene Axin2 and b . total β-catenin in neuroblastoma cell lines. SK-N-BE (2), SK-N-DZ, IMR-32 and Kelly are MYCN amplified neuroblastoma cells with high MycN expression. SH-SY5Y, SK-N-SH and SK-N-FI are non- MYCN amplified neuroblastoma cells expressing relatively low levels of MycN whereas, SK-N-AS and SHEP-1 do not show any MycN expression [ 33 ] c . Quantified protein expression (adjusted to β-actin) of Prickle1 and Vangl2 in neuroblastoma cell lines. Proteins were determined with western blotting. d mRNA expression in neuroblastoma cell lines SK-N-BE (2), SK-N-DZ, SK-N-AS, SH-EP1 and SH-SY5Y, assessed by quantitative real-time PCR, the data displayed is the mean ± S.D. of three determinations

    Article Snippet: The mRNA expression of Prickle1 was not affected after knockdown or overexpression of Vangl2 and similarly, the mRNA expression of Vangl2 was not affected after knockdown or overexpression of Prickle1 in SK-N-AS or SK-N-BE (2) cells (Fig. ).

    Techniques: Expressing, Amplification, Western Blot, Real-time Polymerase Chain Reaction

    Vangl2 alterations affect cell growth, differentiation and active β-catenin expression in neural stem cells in vitro . a siRNA against Vangl2 induced a significant decrease of cell viability compared to control cells transfected with a control siRNA sequence in C17.2 cells (one-way ANOVA with Bonferroni post-test, control vs siRNA Vangl2 P = 0.0004). siRNA against Prickle1 , siRNA against β-catenin , cDNA for Prickle1 or cDNA for Vangl2 caused no change in cell viability. b The mRNA expression of Prickle1 after siRNA or cDNA transfection of Prickle1 , Vangl2 or β-catenin . Only cDNA Prickle1 and siRNA β-catenin induced significant changes in Prickle1 mRNA expression (one-way ANOVA with Bonferroni post-test, control vs cDNA Prickle1 P

    Journal: BMC Cancer

    Article Title: Planar cell polarity gene expression correlates with tumor cell viability and prognostic outcome in neuroblastoma

    doi: 10.1186/s12885-016-2293-2

    Figure Lengend Snippet: Vangl2 alterations affect cell growth, differentiation and active β-catenin expression in neural stem cells in vitro . a siRNA against Vangl2 induced a significant decrease of cell viability compared to control cells transfected with a control siRNA sequence in C17.2 cells (one-way ANOVA with Bonferroni post-test, control vs siRNA Vangl2 P = 0.0004). siRNA against Prickle1 , siRNA against β-catenin , cDNA for Prickle1 or cDNA for Vangl2 caused no change in cell viability. b The mRNA expression of Prickle1 after siRNA or cDNA transfection of Prickle1 , Vangl2 or β-catenin . Only cDNA Prickle1 and siRNA β-catenin induced significant changes in Prickle1 mRNA expression (one-way ANOVA with Bonferroni post-test, control vs cDNA Prickle1 P

    Article Snippet: The mRNA expression of Prickle1 was not affected after knockdown or overexpression of Vangl2 and similarly, the mRNA expression of Vangl2 was not affected after knockdown or overexpression of Prickle1 in SK-N-AS or SK-N-BE (2) cells (Fig. ).

    Techniques: Expressing, In Vitro, Transfection, Sequencing

    Inhibition of Wnt/PCP downstream effector ROCK increases Prickle1 expression and represses active β-catenin. a , b mRNA expression of Prickle1 and Vangl2 after treatment with ROCK inhibitor HA1077 or Y27632 for 72 h; results showed a consistent increase in Prickle1 expression (one-way ANOVA with Bonferroni post-test, SK-N-AS Prickle1: P = 0.0017, control vs HA1077 50 μM P = 0.0023, control vs HA1077 50 μM P = 0.0021, Vangl2: P = 0.0061, control vs HA1077 50 μM P = 0.017 and SH-SY5Y Prickle1 P = 0.019, control vs HA1077 50 μM P = 0.035, control vs HA1077 50 μM P = 0.020 and t -test, SK-N-BE (2) Vangl2 control vs Y27632 80 μM P = 0.0015). Expression of mRNA (relative to the vehicle treated control normalized to the mean expression of the housekeeping genes) was determined by real-time RT-PCR, means with S.D. of triplicates are displayed. c Transcriptional activity of β-catenin after HA1077 exposure; cells were transfected with a TCF/LEF luciferase reporter construct and treated with HA1077 (25 or 50 μM). TOPFlash-dependent activity was significantly reduced as compared with the control (one-way ANOVA with Bonferroni post-test: SK-N-AS P = 0.0144, control vs HA1077 50 μM P = 0.029 and SK-N-BE (2) P = 0.0023, control vs HA1077 50 μM P = 0.012, control vs HA1077 50 μM P = 0.0017). Data represent the mean and SD of three determinations and the experiment was repeated twice. d Protein expression of active β-catenin following HA1077 exposure (96 h, HA1077 25 or 50 μM), determined by western blotting. e mRNA expression of Prickle1 and Vangl2 after knockdown of β-catenin in neuroblastoma cells SK-N-AS and SK-N-BE(2), no significant changes were observed. * P

    Journal: BMC Cancer

    Article Title: Planar cell polarity gene expression correlates with tumor cell viability and prognostic outcome in neuroblastoma

    doi: 10.1186/s12885-016-2293-2

    Figure Lengend Snippet: Inhibition of Wnt/PCP downstream effector ROCK increases Prickle1 expression and represses active β-catenin. a , b mRNA expression of Prickle1 and Vangl2 after treatment with ROCK inhibitor HA1077 or Y27632 for 72 h; results showed a consistent increase in Prickle1 expression (one-way ANOVA with Bonferroni post-test, SK-N-AS Prickle1: P = 0.0017, control vs HA1077 50 μM P = 0.0023, control vs HA1077 50 μM P = 0.0021, Vangl2: P = 0.0061, control vs HA1077 50 μM P = 0.017 and SH-SY5Y Prickle1 P = 0.019, control vs HA1077 50 μM P = 0.035, control vs HA1077 50 μM P = 0.020 and t -test, SK-N-BE (2) Vangl2 control vs Y27632 80 μM P = 0.0015). Expression of mRNA (relative to the vehicle treated control normalized to the mean expression of the housekeeping genes) was determined by real-time RT-PCR, means with S.D. of triplicates are displayed. c Transcriptional activity of β-catenin after HA1077 exposure; cells were transfected with a TCF/LEF luciferase reporter construct and treated with HA1077 (25 or 50 μM). TOPFlash-dependent activity was significantly reduced as compared with the control (one-way ANOVA with Bonferroni post-test: SK-N-AS P = 0.0144, control vs HA1077 50 μM P = 0.029 and SK-N-BE (2) P = 0.0023, control vs HA1077 50 μM P = 0.012, control vs HA1077 50 μM P = 0.0017). Data represent the mean and SD of three determinations and the experiment was repeated twice. d Protein expression of active β-catenin following HA1077 exposure (96 h, HA1077 25 or 50 μM), determined by western blotting. e mRNA expression of Prickle1 and Vangl2 after knockdown of β-catenin in neuroblastoma cells SK-N-AS and SK-N-BE(2), no significant changes were observed. * P

    Article Snippet: The mRNA expression of Prickle1 was not affected after knockdown or overexpression of Vangl2 and similarly, the mRNA expression of Vangl2 was not affected after knockdown or overexpression of Prickle1 in SK-N-AS or SK-N-BE (2) cells (Fig. ).

    Techniques: Inhibition, Expressing, Quantitative RT-PCR, Activity Assay, Transfection, Luciferase, Construct, Western Blot

    Expressions of SNARE complex in submandibular glands ( A ) Expression of VAMP-2, syntaxin-2, syntaxin-4 , and SNAP-23 mRNAs using reverse-transcription PCR (RT-PCR). Relative VAMP-2 ( B ) and syntaxin-4 ( C ) mRNA expression in control and transplanted glands was determined by qPCR. ( D ) Representative co-immunoprecipitation results in control and transplanted glands using VAMP-2 antibody. The band intensities of actin, syntaxin-4, Igκ, myosin regulatory light polypeptide 9, and myosin light polypeptide 6 were normalized to VAMP-2 expression. Quantitative analysis of actin ( E ), syntaxin-4 ( F ), Igκ ( G ), myosin regulatory light polypeptide 9 ( H ), and myosin light polypeptide 6 ( I ) interaction with VAMP-2 in control and transplanted glands. Values are the mean ± S.D. from six independent experiments. * P

    Journal: Bioscience Reports

    Article Title: β-adrenoceptor activation increased VAMP-2 and syntaxin-4 in secretory granules are involved in protein secretion of submandibular gland through the PKA/F-actin pathway

    doi: 10.1042/BSR20171142

    Figure Lengend Snippet: Expressions of SNARE complex in submandibular glands ( A ) Expression of VAMP-2, syntaxin-2, syntaxin-4 , and SNAP-23 mRNAs using reverse-transcription PCR (RT-PCR). Relative VAMP-2 ( B ) and syntaxin-4 ( C ) mRNA expression in control and transplanted glands was determined by qPCR. ( D ) Representative co-immunoprecipitation results in control and transplanted glands using VAMP-2 antibody. The band intensities of actin, syntaxin-4, Igκ, myosin regulatory light polypeptide 9, and myosin light polypeptide 6 were normalized to VAMP-2 expression. Quantitative analysis of actin ( E ), syntaxin-4 ( F ), Igκ ( G ), myosin regulatory light polypeptide 9 ( H ), and myosin light polypeptide 6 ( I ) interaction with VAMP-2 in control and transplanted glands. Values are the mean ± S.D. from six independent experiments. * P

    Article Snippet: The mRNA expression of VAMP-2 and syntaxin-4 did not change ( G,H), whereas the contents of VAMP-2 and syntaxin-4 proteins in the secretory granule fraction were significantly increased ( I–K).

    Techniques: Expressing, Polymerase Chain Reaction, Reverse Transcription Polymerase Chain Reaction, Real-time Polymerase Chain Reaction, Immunoprecipitation

    Expression of VAMP-2 and syntaxin-4 in the secretory granule fraction in isoproterenol-treated and transplanted glands ( A ) Western blot analysis of VAMP-2 and syntaxin-4 in the secretory granule fraction of control and transplanted glands. Quantitative analysis of VAMP-2 ( B ) and syntaxin-4 ( C ) expression. ( D ) Western blot analysis of VAMP-2 and syntaxin-4 in the membrane proteins of control and transplanted glands. Quantitative analysis of VAMP-2 ( E ) and syntaxin-4 ( F ) expression. Relative VAMP-2 ( G ) and syntaxin-4 ( H ) mRNA expression was determined by qPCR. ( I ) Western blot analysis of VAMP-2 and syntaxin-4 in the secretory granule fraction. Quantitative analysis of VAMP-2 ( J ) and syntaxin-4 ( K ) expression normalized to GAPDH. ( L ) Western blot analysis of VAMP-2 and syntaxin-4 in isolated membrane protein fraction. Quantitative analysis of VAMP-2 ( M ) and syntaxin-4 ( N ) expression normalized to occludin. Values are the mean ± S.D. from six independent experiments. * P

    Journal: Bioscience Reports

    Article Title: β-adrenoceptor activation increased VAMP-2 and syntaxin-4 in secretory granules are involved in protein secretion of submandibular gland through the PKA/F-actin pathway

    doi: 10.1042/BSR20171142

    Figure Lengend Snippet: Expression of VAMP-2 and syntaxin-4 in the secretory granule fraction in isoproterenol-treated and transplanted glands ( A ) Western blot analysis of VAMP-2 and syntaxin-4 in the secretory granule fraction of control and transplanted glands. Quantitative analysis of VAMP-2 ( B ) and syntaxin-4 ( C ) expression. ( D ) Western blot analysis of VAMP-2 and syntaxin-4 in the membrane proteins of control and transplanted glands. Quantitative analysis of VAMP-2 ( E ) and syntaxin-4 ( F ) expression. Relative VAMP-2 ( G ) and syntaxin-4 ( H ) mRNA expression was determined by qPCR. ( I ) Western blot analysis of VAMP-2 and syntaxin-4 in the secretory granule fraction. Quantitative analysis of VAMP-2 ( J ) and syntaxin-4 ( K ) expression normalized to GAPDH. ( L ) Western blot analysis of VAMP-2 and syntaxin-4 in isolated membrane protein fraction. Quantitative analysis of VAMP-2 ( M ) and syntaxin-4 ( N ) expression normalized to occludin. Values are the mean ± S.D. from six independent experiments. * P

    Article Snippet: The mRNA expression of VAMP-2 and syntaxin-4 did not change ( G,H), whereas the contents of VAMP-2 and syntaxin-4 proteins in the secretory granule fraction were significantly increased ( I–K).

    Techniques: Expressing, Western Blot, Real-time Polymerase Chain Reaction, Isolation

    Integrative miRNA–mRNA analysis. ( A ) Illustration of the analysis workflow. ( B ) Tallies of significant miRNA and mRNA probes after filtering using Tukey's P -value (

    Journal: Journal of Cell Science

    Article Title: Matched miRNA and mRNA signatures from an hESC-based in vitro model of pancreatic differentiation reveal novel regulatory interactions

    doi: 10.1242/jcs.123570

    Figure Lengend Snippet: Integrative miRNA–mRNA analysis. ( A ) Illustration of the analysis workflow. ( B ) Tallies of significant miRNA and mRNA probes after filtering using Tukey's P -value (

    Article Snippet: The miRNA expression data were acquired on the Illumina Human v2 miRNA platform (with 1146 miRNA probes) and the mRNA expression data was acquired on the Illumina Human HT-12 v4 gene expression microarray ( > 40,000 mRNA transcripts), using 200 ng total RNA per sample each.

    Techniques:

    Gene expression changes in CD28- vs CD86-silenced cells are consistent with regulation of both distinct and common pathways, including expression of IRF4. (A) Gene set enrichment analysis showing upregulated (top) and downregulated (bottom) gene sets in shCD28- (blue) and shCD86-treated (red) myeloma cells. For each gene set, the enrichment score is shown above the ranked change in gene expression, where genes that overlap the gene set are denoted by blue and red ticks for shCD28 and shCD86, respectively. (B) qRT-PCR showing IRF4 mRNA levels when CD28 or CD86 was silenced in MM.1s or 8226 cells. (C) Representative western blots showing IRF4 levels with silencing of CD28 or CD86 in cell lines indicated at different time points. (D) Integrin levels were measured via qRT-PCR ( ITGB7 and ITGB1 ; left). Representative histograms showing ITGβ1 and ITGβ7 on day 4 after shRNA treatment (right). For qRT-PCR, all data are normalized to β-actin as an endogenous control and then compared relative to mRNA levels in pLKO.1 empty vector control. RNA was extracted at day 3 postinfection. Data shown are mean ± SEM of at least 3 independent experiments. Histograms showing surface levels of indicated molecules. Gray histograms at left represent unstained or isotype controls. Flow cytometry data shown are from day 4 postinfection with lentiviral vectors. Flow cytometry and western blot data shown are representative of at least 3 independent experiments. (E) Cell adhesion 3 days postinfection with lentivirus containing the indicated shRNA. Myeloma cells stained with calcein AM were cocultured with HS-5 cells for 2 hours. Fluorescence was measured (485/528 emission/excitation) with BioTek Synergy H1 multiwell plate reader, and data are presented as fluorescence relative to pLKO.1 controls (mean ± SEM). Prewash readings were taken to ensure similar numbers of live cells were added to each well. All samples were plated in triplicate. Data are mean of 3 independent experiments. GAPDH, glyceraldehyde-3-phosphate dehydrogenase; GX, gene expression changes; RFU, relative fluorescence unit.

    Journal: Blood Advances

    Article Title: CD86 regulates myeloma cell survival

    doi: 10.1182/bloodadvances.2017011601

    Figure Lengend Snippet: Gene expression changes in CD28- vs CD86-silenced cells are consistent with regulation of both distinct and common pathways, including expression of IRF4. (A) Gene set enrichment analysis showing upregulated (top) and downregulated (bottom) gene sets in shCD28- (blue) and shCD86-treated (red) myeloma cells. For each gene set, the enrichment score is shown above the ranked change in gene expression, where genes that overlap the gene set are denoted by blue and red ticks for shCD28 and shCD86, respectively. (B) qRT-PCR showing IRF4 mRNA levels when CD28 or CD86 was silenced in MM.1s or 8226 cells. (C) Representative western blots showing IRF4 levels with silencing of CD28 or CD86 in cell lines indicated at different time points. (D) Integrin levels were measured via qRT-PCR ( ITGB7 and ITGB1 ; left). Representative histograms showing ITGβ1 and ITGβ7 on day 4 after shRNA treatment (right). For qRT-PCR, all data are normalized to β-actin as an endogenous control and then compared relative to mRNA levels in pLKO.1 empty vector control. RNA was extracted at day 3 postinfection. Data shown are mean ± SEM of at least 3 independent experiments. Histograms showing surface levels of indicated molecules. Gray histograms at left represent unstained or isotype controls. Flow cytometry data shown are from day 4 postinfection with lentiviral vectors. Flow cytometry and western blot data shown are representative of at least 3 independent experiments. (E) Cell adhesion 3 days postinfection with lentivirus containing the indicated shRNA. Myeloma cells stained with calcein AM were cocultured with HS-5 cells for 2 hours. Fluorescence was measured (485/528 emission/excitation) with BioTek Synergy H1 multiwell plate reader, and data are presented as fluorescence relative to pLKO.1 controls (mean ± SEM). Prewash readings were taken to ensure similar numbers of live cells were added to each well. All samples were plated in triplicate. Data are mean of 3 independent experiments. GAPDH, glyceraldehyde-3-phosphate dehydrogenase; GX, gene expression changes; RFU, relative fluorescence unit.

    Article Snippet: RNA was isolated using the Qiagen RNEasy Kit as described and quality control tested at the Emory Integrated Genomics Core, and 1 µg was sent to Hudson α for RNA sequencing (RNA-seq) library construction using the Illumina TruSeq messenger RNA (mRNA) protocol.

    Techniques: Expressing, Quantitative RT-PCR, Western Blot, shRNA, Plasmid Preparation, Flow Cytometry, Cytometry, Staining, Fluorescence

    PIK3CA expression level increases from corresponding primary to metastatic lesions. ( a ) The PIK3CA mRNA expression level increases significantly from the primary tumors to metastatic lesions measured within same patient. ( b ) Binary directional shift in PIK3CA expression level in the metastasis compared to the primary tumor. The absence of mutation is most likely to increase PIK3CA expression towards metastatic state, while half of the cases with mutations also display reduced PIK3CA expression in the metastatic lesions. Number of cases is indicated as affected cases/total cases in each group. ( c ) The PI3K mRNA signature score defined by Gustafson et al . 29 and ( d ) expression of p-AKT/AKT comparing the paired samples of corresponding primary and metastatic tumors. For simplicity, first metastatic lesion (M1) was used as comparison when multiple metastases were available. Statistical test: Mann-Whitney U test.

    Journal: Scientific Reports

    Article Title: PIK3CA exon9 mutations associate with reduced survival, and are highly concordant between matching primary tumors and metastases in endometrial cancer

    doi: 10.1038/s41598-017-10717-z

    Figure Lengend Snippet: PIK3CA expression level increases from corresponding primary to metastatic lesions. ( a ) The PIK3CA mRNA expression level increases significantly from the primary tumors to metastatic lesions measured within same patient. ( b ) Binary directional shift in PIK3CA expression level in the metastasis compared to the primary tumor. The absence of mutation is most likely to increase PIK3CA expression towards metastatic state, while half of the cases with mutations also display reduced PIK3CA expression in the metastatic lesions. Number of cases is indicated as affected cases/total cases in each group. ( c ) The PI3K mRNA signature score defined by Gustafson et al . 29 and ( d ) expression of p-AKT/AKT comparing the paired samples of corresponding primary and metastatic tumors. For simplicity, first metastatic lesion (M1) was used as comparison when multiple metastases were available. Statistical test: Mann-Whitney U test.

    Article Snippet: Metastatic lesions show increased PIK3CA mRNA expression independent of mutation status, and increased p-AKT/AKT protein levels dependent of PIK3CA mutations We investigated the mRNA expression of PIK3CA , and found it increased from primary tumor to paired metastases within paired samples (p = 0.031; Fig. ).

    Techniques: Expressing, Mutagenesis, MANN-WHITNEY