taqman universal pcr master mix  (Thermo Fisher)


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    TaqMan Universal PCR Master Mix individually packaged
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    Alternative Product Try TaqMan Fast Advanced Master Mix our highest performance probe based master mix With TaqMan Fast Advanced Master Mix we ve taken the best of TaqMan Universal PCR Master Mix and added additional capabilities for your gene expression analysis Applied Biosystems TaqMan Universal PCR Master Mix is the ideal reagent solution when you need a Master Mix for multiple 5 nuclease DNA applications Applied Biosystems reagents have been validated with TaqMan Assays and Applied Biosystems real time systems to ensure sensitive accurate and reliable performance every time • Contains AmpliTaq Gold DNA polymerase to provide a better yield and a more robust 5 nuclease assay than AmpliTaq DNA polymerase • Includes a passive internal reference based on proprietary ROX dye for superb precision on Applied Biosystems real time PCR instruments • Buffer enhancements guarantee performance and reliability in all applications even with G C rich sequences • AmpErase UNG protects against subsequent re amplification from PCR products containing dU to minimize carry over contamination • Rapid assay development guidelines are provided to minimize optimization time
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    4305719
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    Enzymes & Master Mixes for Real-Time PCR|Industrial & Applied Science|PCR & Real-Time PCR|PCR-Based Drug Discovery Assays|Pharma & Biopharma|RNAi, Epigenetics & Non-Coding RNA Research|Real Time PCR (qPCR)|Real Time PCR-Based Gene Expression Profiling|Real Time PCR-Based miRNA Analysis|miRNA & Non-Coding RNA Analysis|Target & Lead Identification & Validation|Gene Expression Analysis & Genotyping
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    Structured Review

    Thermo Fisher taqman universal pcr master mix
    Results obtained in cross-reactivity tests performed with DNA isolates from 23 animal species with 5 commercial master mixes. ( A ) QuantiTect® Multiplex <t>PCR</t> NoROX Master Mix (Qiagen), ( B ) <t>TaqMan®</t> Universal PCR Master Mix (Applied Biosystems), ( C ) GoTaq® Probe qPCR Master Mix (Promega), ( D ) PerfeCTa® qPCR ToughMix TM , Low ROX TM (Quanta Biosciences) and E) Takyon TM No Rox Probe MasterMix dTTP Blue (Eurogentec).
    Alternative Product Try TaqMan Fast Advanced Master Mix our highest performance probe based master mix With TaqMan Fast Advanced Master Mix we ve taken the best of TaqMan Universal PCR Master Mix and added additional capabilities for your gene expression analysis Applied Biosystems TaqMan Universal PCR Master Mix is the ideal reagent solution when you need a Master Mix for multiple 5 nuclease DNA applications Applied Biosystems reagents have been validated with TaqMan Assays and Applied Biosystems real time systems to ensure sensitive accurate and reliable performance every time • Contains AmpliTaq Gold DNA polymerase to provide a better yield and a more robust 5 nuclease assay than AmpliTaq DNA polymerase • Includes a passive internal reference based on proprietary ROX dye for superb precision on Applied Biosystems real time PCR instruments • Buffer enhancements guarantee performance and reliability in all applications even with G C rich sequences • AmpErase UNG protects against subsequent re amplification from PCR products containing dU to minimize carry over contamination • Rapid assay development guidelines are provided to minimize optimization time
    https://www.bioz.com/result/taqman universal pcr master mix/product/Thermo Fisher
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    Images

    1) Product Images from "Sika deer (Cervus nippon)-specific real-time PCR method to detect fraudulent labelling of meat and meat products"

    Article Title: Sika deer (Cervus nippon)-specific real-time PCR method to detect fraudulent labelling of meat and meat products

    Journal: Scientific Reports

    doi: 10.1038/s41598-018-25299-7

    Results obtained in cross-reactivity tests performed with DNA isolates from 23 animal species with 5 commercial master mixes. ( A ) QuantiTect® Multiplex PCR NoROX Master Mix (Qiagen), ( B ) TaqMan® Universal PCR Master Mix (Applied Biosystems), ( C ) GoTaq® Probe qPCR Master Mix (Promega), ( D ) PerfeCTa® qPCR ToughMix TM , Low ROX TM (Quanta Biosciences) and E) Takyon TM No Rox Probe MasterMix dTTP Blue (Eurogentec).
    Figure Legend Snippet: Results obtained in cross-reactivity tests performed with DNA isolates from 23 animal species with 5 commercial master mixes. ( A ) QuantiTect® Multiplex PCR NoROX Master Mix (Qiagen), ( B ) TaqMan® Universal PCR Master Mix (Applied Biosystems), ( C ) GoTaq® Probe qPCR Master Mix (Promega), ( D ) PerfeCTa® qPCR ToughMix TM , Low ROX TM (Quanta Biosciences) and E) Takyon TM No Rox Probe MasterMix dTTP Blue (Eurogentec).

    Techniques Used: Multiplex Assay, Polymerase Chain Reaction, Real-time Polymerase Chain Reaction

    2) Product Images from "Integrated analysis of microRNA and mRNA expression profiles in physiological myelopoiesis: role of hsa-mir-299-5p in CD34+ progenitor cells commitment"

    Article Title: Integrated analysis of microRNA and mRNA expression profiles in physiological myelopoiesis: role of hsa-mir-299-5p in CD34+ progenitor cells commitment

    Journal: Cell Death & Disease

    doi: 10.1038/cddis.2010.5

    Anti-miRNA inhibitor molecule transfections. ( a ) TaqMan real-time PCR evaluation of mature hsa-miR-299-5p microRNA expression after 24, 72 and 96 h of cell culture in the presence of TPO (100 ng/ml). Data were obtained using as calibrator the RNA of the same sample extracted immediately after CD34 HPC purification and RNU6b as endogenous control. Cells were electroporated with hsa-miR-299-5p inhibitor after 3 days of culture. ( b ) TaqMan real-time PCR mature hsa-miR-299-5p expression after single transient transfection of its inhibitor molecule, through single nucleoporation with the Amaxa Nucleofector device. Expression withdrawal was monitored after one and ten days from nucleofection. Data were obtained using as calibrator the nucleofection solution-treated sample (nuc) and RNU6b as endogenous control. ( c ) Colony-forming capacity of HPCs transfected with hsa-miR-299-5p Anti-miR miRNA inhibitor (anti-299-5p), compared with Anti-miR miRNA inhibitor-negative control #1 (anti-NC1)-transfected cells and cells electroporated with the nucleofection solution only (nuc). Mean±S.D. from three independent experiments. Asterisk indicates a t -test P -value⩽0.001. BFU-E: erythrocyte burst-forming unit; CFU-E: erythrocyte colony-forming unit; GM-CFU: granulo-monocyte colony-forming unit; G-CFU: granulocyte colony-forming unit; M-CFU: monocyte colony-forming unit; GEMM-CFU: granulocyte-erythrocyte-monocyte-macrophage colony-forming unit. ( d ) Megakaryocytic colony-forming capacity of HPCs transfected with hsa-miR-299-5p Anti-miR miRNA Inhibitor (anti-299-5p), compared with anti-miR miRNA inhibitor-negative control #1 (anti-NC1)-transfected cells and cells electroporated with the nucleofection solution only (nuc). Mean±S.D. from three independent experiments. Asterisk indicates a t -test P -value⩽0.001
    Figure Legend Snippet: Anti-miRNA inhibitor molecule transfections. ( a ) TaqMan real-time PCR evaluation of mature hsa-miR-299-5p microRNA expression after 24, 72 and 96 h of cell culture in the presence of TPO (100 ng/ml). Data were obtained using as calibrator the RNA of the same sample extracted immediately after CD34 HPC purification and RNU6b as endogenous control. Cells were electroporated with hsa-miR-299-5p inhibitor after 3 days of culture. ( b ) TaqMan real-time PCR mature hsa-miR-299-5p expression after single transient transfection of its inhibitor molecule, through single nucleoporation with the Amaxa Nucleofector device. Expression withdrawal was monitored after one and ten days from nucleofection. Data were obtained using as calibrator the nucleofection solution-treated sample (nuc) and RNU6b as endogenous control. ( c ) Colony-forming capacity of HPCs transfected with hsa-miR-299-5p Anti-miR miRNA inhibitor (anti-299-5p), compared with Anti-miR miRNA inhibitor-negative control #1 (anti-NC1)-transfected cells and cells electroporated with the nucleofection solution only (nuc). Mean±S.D. from three independent experiments. Asterisk indicates a t -test P -value⩽0.001. BFU-E: erythrocyte burst-forming unit; CFU-E: erythrocyte colony-forming unit; GM-CFU: granulo-monocyte colony-forming unit; G-CFU: granulocyte colony-forming unit; M-CFU: monocyte colony-forming unit; GEMM-CFU: granulocyte-erythrocyte-monocyte-macrophage colony-forming unit. ( d ) Megakaryocytic colony-forming capacity of HPCs transfected with hsa-miR-299-5p Anti-miR miRNA Inhibitor (anti-299-5p), compared with anti-miR miRNA inhibitor-negative control #1 (anti-NC1)-transfected cells and cells electroporated with the nucleofection solution only (nuc). Mean±S.D. from three independent experiments. Asterisk indicates a t -test P -value⩽0.001

    Techniques Used: Transfection, Real-time Polymerase Chain Reaction, Expressing, Cell Culture, Purification, Negative Control

    Pre-miR miRNA Precursor Molecule transfections. ( a ) TaqMan real-time PCR of mature hsa-miR-299-5p expression after single transient transfection of its precursor molecule through the Amaxa Nucleofector device. Hsa-miR-299-5p expression was monitored at different time points during in vitro culture using the nucleofection solution-treated sample (nuc) as calibrator and RNU6b as endogenous control. ( b ) Cytofluorimetric evaluation of the differentiation surface markers' expression: CD235a for erythroid differentiation, CD41a as indicator of megakaryocytic commitment, CD14 distinguishing monocytic differentiation and CD66b reflecting granulocytic cell fate. The surface markers' expression was checked after seven days of culture and each bar represents the fold change of the percentage of positivity normalized onto the pre-miR miRNA precursor molecule-negative control # 1 (NC1)-treated sample. Asterisk indicates a t -test P -value ⩽0.001. ( c ) Colony-forming capacity of HPCs transfected with pre-miR miRNA precursor molecule (299-5p), when compared with Pre-miR miRNA Precursor molecule-negative control # 1 (NC1)-transfected cells and with cells electroporated with the nucleofection solution only (nuc). Mean±S.D. from four independent experiments. BFU-E: erythrocyte burst-forming unit; CFU-E: erythrocyte colony-forming unit; GM-CFU: granulo-monocyte colony-forming unit; G-CFU: granulocyte colony-forming unit; M-CFU: monocyte colony-forming unit; GEMM-CFU: granulocyte-erythrocyte-monocyte-macrophage colony-forming unit. Asterisk indicates a t -test P -value ⩽0.001. ( d ) Megakaryocytic colony-forming capacity of HPCs transfected with pre-miR miRNA precursor molecule (299-5p), when compared with pre-miR miRNA precursor molecule-negative control # 1 (NC1)-transfected cells and cells electroporated with the nucleofection solution only (nuc). Mean±S.D. from four independent experiments. Asterisk indicates a t -test P -value ⩽0.001
    Figure Legend Snippet: Pre-miR miRNA Precursor Molecule transfections. ( a ) TaqMan real-time PCR of mature hsa-miR-299-5p expression after single transient transfection of its precursor molecule through the Amaxa Nucleofector device. Hsa-miR-299-5p expression was monitored at different time points during in vitro culture using the nucleofection solution-treated sample (nuc) as calibrator and RNU6b as endogenous control. ( b ) Cytofluorimetric evaluation of the differentiation surface markers' expression: CD235a for erythroid differentiation, CD41a as indicator of megakaryocytic commitment, CD14 distinguishing monocytic differentiation and CD66b reflecting granulocytic cell fate. The surface markers' expression was checked after seven days of culture and each bar represents the fold change of the percentage of positivity normalized onto the pre-miR miRNA precursor molecule-negative control # 1 (NC1)-treated sample. Asterisk indicates a t -test P -value ⩽0.001. ( c ) Colony-forming capacity of HPCs transfected with pre-miR miRNA precursor molecule (299-5p), when compared with Pre-miR miRNA Precursor molecule-negative control # 1 (NC1)-transfected cells and with cells electroporated with the nucleofection solution only (nuc). Mean±S.D. from four independent experiments. BFU-E: erythrocyte burst-forming unit; CFU-E: erythrocyte colony-forming unit; GM-CFU: granulo-monocyte colony-forming unit; G-CFU: granulocyte colony-forming unit; M-CFU: monocyte colony-forming unit; GEMM-CFU: granulocyte-erythrocyte-monocyte-macrophage colony-forming unit. Asterisk indicates a t -test P -value ⩽0.001. ( d ) Megakaryocytic colony-forming capacity of HPCs transfected with pre-miR miRNA precursor molecule (299-5p), when compared with pre-miR miRNA precursor molecule-negative control # 1 (NC1)-transfected cells and cells electroporated with the nucleofection solution only (nuc). Mean±S.D. from four independent experiments. Asterisk indicates a t -test P -value ⩽0.001

    Techniques Used: Transfection, Real-time Polymerase Chain Reaction, Expressing, In Vitro, Negative Control

    MicroRNAs oppositely regulated during myeloid differentiation. Twenty-three microRNAs (indicated with the prefix miR-) show either up- or downregulation greater than four in at least one precursor population when compared with the CD34 HPCs; 17 showed a significant increased expression with an RQ higher than four, 15 a significant decreased expression with an RQ lower than −4 and concomitantly a counter-regulation in at least one other precursor cell context. TaqMan real-time PCR reactions were carried out using the TaqMan MicroRNA Assays Human Panel Early Access Kit. Delta-delta-CTs and RQs were calculated for each detector using the CD34 HPC sample as the calibrator and hsa-miR-let-7a as the endogenous control
    Figure Legend Snippet: MicroRNAs oppositely regulated during myeloid differentiation. Twenty-three microRNAs (indicated with the prefix miR-) show either up- or downregulation greater than four in at least one precursor population when compared with the CD34 HPCs; 17 showed a significant increased expression with an RQ higher than four, 15 a significant decreased expression with an RQ lower than −4 and concomitantly a counter-regulation in at least one other precursor cell context. TaqMan real-time PCR reactions were carried out using the TaqMan MicroRNA Assays Human Panel Early Access Kit. Delta-delta-CTs and RQs were calculated for each detector using the CD34 HPC sample as the calibrator and hsa-miR-let-7a as the endogenous control

    Techniques Used: Expressing, Real-time Polymerase Chain Reaction

    3) Product Images from "Dual role of the caspase enzymes in satellite cells from aged and young subjects"

    Article Title: Dual role of the caspase enzymes in satellite cells from aged and young subjects

    Journal: Cell Death & Disease

    doi: 10.1038/cddis.2013.472

    Expression levels of genes representative of the apoptosis pathway, analysed with RT-PCR using TaqMan low density arrays. Data from the log 10 of relative quantifications of the transcripts for the target genes versus GAPDH gene expression are represented as the aged SCs to young SCs ratios, as indicated, following in vitro culture for 4 h ( a ), 24 h ( b ), 48 h ( c ) and 72 h ( d )
    Figure Legend Snippet: Expression levels of genes representative of the apoptosis pathway, analysed with RT-PCR using TaqMan low density arrays. Data from the log 10 of relative quantifications of the transcripts for the target genes versus GAPDH gene expression are represented as the aged SCs to young SCs ratios, as indicated, following in vitro culture for 4 h ( a ), 24 h ( b ), 48 h ( c ) and 72 h ( d )

    Techniques Used: Expressing, Reverse Transcription Polymerase Chain Reaction, In Vitro

    4) Product Images from "Insights into the complex regulation of rpoS in Borrelia burgdorferi"

    Article Title: Insights into the complex regulation of rpoS in Borrelia burgdorferi

    Journal: Molecular Microbiology

    doi: 10.1111/j.1365-2958.2007.05813.x

    Quantitative RT-PCR analysis of rpoS and ospC transcripts and immunoblot analysis of RpoS and OspC as cell density increases RNA was extracted from B. burgdorferi strains B31-A3 (grey bars), A3 ntrA (black bars) and A3 hk2 (white bars) as spirochete density increased and transcripts were quantified using specific primers and probes with the Taqman system. Values have been normalized to the internal control, flaB. Data presented represents averages of three assays performed in quadruplicate. Error bars represent standard deviation. A. QRT-PCR analysis of rpoS as cell density increased. Fold changes are expressed relative to the initial inoculum. B. QRT-PCR analysis of ospC as cell density increased. Fold changes are expressed relative to the initial inoculum. C. QRT-PCR analysis of rpoS (hatched bars) and ospC (black bars) transcripts in A3 ntrA relative to B31-A3. Fold changes are expressed compared with B31-A3 at corresponding cell densities. D. QRT-PCR analysis of rpoS (hatched bars) and ospC (black bars) transcripts in A3 hk2 relative to B31-A3. Fold changes are expressed compared to the B31-A3 at corresponding cell densities. E. Immunoblot analysis of RpoS and OspC levels in B. burgdorferi strains B31-A3, A3 ntrA and A3 hk2 as cell density increased. Whole-cell lysates of B. burgdorferi strains equivalent to approximately 8 × 10 7 −1 × 10 8 cells were separated on 12% Tris-glycine gels, immobilized on nitrocellulose membranes and probed with antiserum specific for the antigens indicated on the left. FlaB serves as a loading control to demonstrate equivalent protein amounts between samples. Cell densities are indicated at the top of each lane, and positive controls for the A3 ntrA samples are indicated by a plus sign (+).
    Figure Legend Snippet: Quantitative RT-PCR analysis of rpoS and ospC transcripts and immunoblot analysis of RpoS and OspC as cell density increases RNA was extracted from B. burgdorferi strains B31-A3 (grey bars), A3 ntrA (black bars) and A3 hk2 (white bars) as spirochete density increased and transcripts were quantified using specific primers and probes with the Taqman system. Values have been normalized to the internal control, flaB. Data presented represents averages of three assays performed in quadruplicate. Error bars represent standard deviation. A. QRT-PCR analysis of rpoS as cell density increased. Fold changes are expressed relative to the initial inoculum. B. QRT-PCR analysis of ospC as cell density increased. Fold changes are expressed relative to the initial inoculum. C. QRT-PCR analysis of rpoS (hatched bars) and ospC (black bars) transcripts in A3 ntrA relative to B31-A3. Fold changes are expressed compared with B31-A3 at corresponding cell densities. D. QRT-PCR analysis of rpoS (hatched bars) and ospC (black bars) transcripts in A3 hk2 relative to B31-A3. Fold changes are expressed compared to the B31-A3 at corresponding cell densities. E. Immunoblot analysis of RpoS and OspC levels in B. burgdorferi strains B31-A3, A3 ntrA and A3 hk2 as cell density increased. Whole-cell lysates of B. burgdorferi strains equivalent to approximately 8 × 10 7 −1 × 10 8 cells were separated on 12% Tris-glycine gels, immobilized on nitrocellulose membranes and probed with antiserum specific for the antigens indicated on the left. FlaB serves as a loading control to demonstrate equivalent protein amounts between samples. Cell densities are indicated at the top of each lane, and positive controls for the A3 ntrA samples are indicated by a plus sign (+).

    Techniques Used: Quantitative RT-PCR, Standard Deviation

    Quantitative RT-PCR analysis of rpoS and ospC transcripts and immunoblot analysis of RpoS and OspC following an increase in growth temperature from 23°C to 34°C. RNA was extracted from B. burgdorferi strains B31-A3 (grey bars), A3 ntrA (black bars) and A3 hk2 (white bars) grown at 23°C and following a temperature shift to 34°C, and transcripts were quantified using specific primers and probes with the Taqman system. Values have been normalized to the internal control, flaB. Data presented represents averages of three assays performed in quadruplicate. Error bars represent standard deviation. A. QRT-PCR analysis of rpoS following a temperature shift. Fold changes are expressed relative to spirochetes grown at 23°C. B. QRT-PCR analysis of ospC following a temperature shift. Fold changes are expressed relative to spirochetes grown at 23°C. C. QRT-PCR analysis of rpoS (hatched bars) and ospC (black bars) transcripts in A3 ntrA relative to B31-A3. Fold changes are expressed compared with the B31-A3 at corresponding time points. D. QRT-PCR analysis of rpoS (hatched bars) and ospC (black bars) transcripts in A3 hk2 relative to B31-A3. Fold changes are expressed compared with the B31-A3 at corresponding time points. E. Growth curves of B31-A3 (grey triangles), A3 ntrA (black diamonds) and A3 hk2 (open circles) following a temperature shift from 23°C to 34°C. F. Immunoblot analysis of RpoS and OspC levels in B. burgdorferi strains B31-A3, A3 ntrA and A3 hk2 following an increase in growth temperature from 23°C to 34°C. Whole-cell lysates of B. burgdorferi strains equivalent to approximately 8 × 10 7 −1 × 10 8 cells were separated on 12% Tris-glycine gels, immobilized on nitrocellulose membranes and probed with antiserum specific for the antigens indicated on the left. FlaB serves as a loading control to demonstrate equivalent protein amounts between samples. Time points are indicated at the top of each lane, and positive controls for the A3 ntrA samples are indicated by a plus sign (+).
    Figure Legend Snippet: Quantitative RT-PCR analysis of rpoS and ospC transcripts and immunoblot analysis of RpoS and OspC following an increase in growth temperature from 23°C to 34°C. RNA was extracted from B. burgdorferi strains B31-A3 (grey bars), A3 ntrA (black bars) and A3 hk2 (white bars) grown at 23°C and following a temperature shift to 34°C, and transcripts were quantified using specific primers and probes with the Taqman system. Values have been normalized to the internal control, flaB. Data presented represents averages of three assays performed in quadruplicate. Error bars represent standard deviation. A. QRT-PCR analysis of rpoS following a temperature shift. Fold changes are expressed relative to spirochetes grown at 23°C. B. QRT-PCR analysis of ospC following a temperature shift. Fold changes are expressed relative to spirochetes grown at 23°C. C. QRT-PCR analysis of rpoS (hatched bars) and ospC (black bars) transcripts in A3 ntrA relative to B31-A3. Fold changes are expressed compared with the B31-A3 at corresponding time points. D. QRT-PCR analysis of rpoS (hatched bars) and ospC (black bars) transcripts in A3 hk2 relative to B31-A3. Fold changes are expressed compared with the B31-A3 at corresponding time points. E. Growth curves of B31-A3 (grey triangles), A3 ntrA (black diamonds) and A3 hk2 (open circles) following a temperature shift from 23°C to 34°C. F. Immunoblot analysis of RpoS and OspC levels in B. burgdorferi strains B31-A3, A3 ntrA and A3 hk2 following an increase in growth temperature from 23°C to 34°C. Whole-cell lysates of B. burgdorferi strains equivalent to approximately 8 × 10 7 −1 × 10 8 cells were separated on 12% Tris-glycine gels, immobilized on nitrocellulose membranes and probed with antiserum specific for the antigens indicated on the left. FlaB serves as a loading control to demonstrate equivalent protein amounts between samples. Time points are indicated at the top of each lane, and positive controls for the A3 ntrA samples are indicated by a plus sign (+).

    Techniques Used: Quantitative RT-PCR, Standard Deviation

    Quantitative RT-PCR analysis of rpoS and ospC transcripts following an increase in growth temperature from 23°C to 34°C. RNA was extracted from B. burgdorferi strains B31-A3 (low-passage, white bars) and B31-A (high-passage, black bars) grown at 23°C, and at various time points following a temperature shift to 34°C. Levels of transcripts were measured with specific primer/probe sets using Taqman, and values have been normalized to the internal control, flaB. Data presented represents averages of three assays performed in quadruplicate. Fold changes are expressed relative to spirochetes grown at 23°C. Error bars represent standard deviation. A. QRT-PCR analysis of rpoS following a temperature shift. B. QRT-PCR analysis of ospC following a temperature shift. C. Growth curves of B31-A3 (white squares) and B31-A (black triangles) following a temperature shift from 23 to 34°C.
    Figure Legend Snippet: Quantitative RT-PCR analysis of rpoS and ospC transcripts following an increase in growth temperature from 23°C to 34°C. RNA was extracted from B. burgdorferi strains B31-A3 (low-passage, white bars) and B31-A (high-passage, black bars) grown at 23°C, and at various time points following a temperature shift to 34°C. Levels of transcripts were measured with specific primer/probe sets using Taqman, and values have been normalized to the internal control, flaB. Data presented represents averages of three assays performed in quadruplicate. Fold changes are expressed relative to spirochetes grown at 23°C. Error bars represent standard deviation. A. QRT-PCR analysis of rpoS following a temperature shift. B. QRT-PCR analysis of ospC following a temperature shift. C. Growth curves of B31-A3 (white squares) and B31-A (black triangles) following a temperature shift from 23 to 34°C.

    Techniques Used: Quantitative RT-PCR, Standard Deviation

    5) Product Images from "A novel, high-performance random array platform for quantitative gene expression profiling"

    Article Title: A novel, high-performance random array platform for quantitative gene expression profiling

    Journal: Genome Research

    doi: 10.1101/gr.2739104

    Correlation of array matrix data to quantitative real-time PCR. Labeled RNA samples were made from human and brain total RNA. These were hybridized to separate array matrices containing 633 human genes. Six technical replicates were included for each sample. Twenty-one genes from this list were selected for analysis by TaqMan quantitative real-time PCR. A scatter plot of hybridization intensities of the liver and brain samples on the array matrix is shown in A . Genes selected for further analysis are shaded orange. A scatter plot of log-transformed hybridization signal ratios as determined by the two methods is shown in B .
    Figure Legend Snippet: Correlation of array matrix data to quantitative real-time PCR. Labeled RNA samples were made from human and brain total RNA. These were hybridized to separate array matrices containing 633 human genes. Six technical replicates were included for each sample. Twenty-one genes from this list were selected for analysis by TaqMan quantitative real-time PCR. A scatter plot of hybridization intensities of the liver and brain samples on the array matrix is shown in A . Genes selected for further analysis are shaded orange. A scatter plot of log-transformed hybridization signal ratios as determined by the two methods is shown in B .

    Techniques Used: Real-time Polymerase Chain Reaction, Labeling, Hybridization, Transformation Assay

    6) Product Images from "Temporal Analysis of Coxiella burnetii Morphological Differentiation"

    Article Title: Temporal Analysis of Coxiella burnetii Morphological Differentiation

    Journal: Journal of Bacteriology

    doi: 10.1128/JB.186.21.7344-7352.2004

    Relative expression levels of selected C. burnetii genes during morphological differentiation as detected by quantitative RT-PCR. Assays were performed using TaqMan primers and probes specific for each gene. Vero cell monolayers were incubated with purified SCV for 1 h to allow for adherence and internalization. Extracellular organisms were then washed from cell monolayers, and fresh medium was added. This time was designated as 0 h p.i. Total RNA was extracted at the indicated times. Transcriptional activity is expressed as relative expression, with transcript copy number normalized to the number of C. burnetii genomes present in each sample. The results are expressed as the mean from three experiments, with error bars representing the standard error of the mean.
    Figure Legend Snippet: Relative expression levels of selected C. burnetii genes during morphological differentiation as detected by quantitative RT-PCR. Assays were performed using TaqMan primers and probes specific for each gene. Vero cell monolayers were incubated with purified SCV for 1 h to allow for adherence and internalization. Extracellular organisms were then washed from cell monolayers, and fresh medium was added. This time was designated as 0 h p.i. Total RNA was extracted at the indicated times. Transcriptional activity is expressed as relative expression, with transcript copy number normalized to the number of C. burnetii genomes present in each sample. The results are expressed as the mean from three experiments, with error bars representing the standard error of the mean.

    Techniques Used: Expressing, Quantitative RT-PCR, Incubation, Purification, Activity Assay

    7) Product Images from "FIAT represses ATF4-mediated transcription to regulate bone mass in transgenic mice"

    Article Title: FIAT represses ATF4-mediated transcription to regulate bone mass in transgenic mice

    Journal: The Journal of Cell Biology

    doi: 10.1083/jcb.200412139

    Expression of osteoblast expression markers. RNA was extracted from 3-mo-old calvaria, reverse-transcribed, and amplified with specific TaqMan probes using real-time PCR. Relative expression between wild-type (Wt) and transgenic (Tg) animals was calculated by the relative standard curve method and normalized to GAPDH. *, P
    Figure Legend Snippet: Expression of osteoblast expression markers. RNA was extracted from 3-mo-old calvaria, reverse-transcribed, and amplified with specific TaqMan probes using real-time PCR. Relative expression between wild-type (Wt) and transgenic (Tg) animals was calculated by the relative standard curve method and normalized to GAPDH. *, P

    Techniques Used: Expressing, Amplification, Real-time Polymerase Chain Reaction, Transgenic Assay

    8) Product Images from "SIRT1 Inhibition Alleviates Gene Silencing in Fragile X Mental Retardation Syndrome"

    Article Title: SIRT1 Inhibition Alleviates Gene Silencing in Fragile X Mental Retardation Syndrome

    Journal: PLoS Genetics

    doi: 10.1371/journal.pgen.1000017

    The effect of nicotinamide and splitomicin on FMR1 gene expression in unaffected and FXS cell lines. (A). Lymphoblastoid cells from an unaffected individual (GM02168), individuals with FXS (GM06897 and GM03200B) treated with the indicated concentrations of nicotinamide. (B and C) Lymphoblastoid cells from an unaffected individual (GM02168), individuals with FXS (GM06897, GM03200B, GM09145 and GM04025) treated with the indicated concentrations of splitomicin. (D) FXS fibroblasts (GM05131 and GM05848) treated with 700 µM splitomicin. FMR1 mRNA levels were measured by real time PCR using Taqman primer-probe mixes. The FMR1 expression in patient cells was plotted as a percentage of the FMR1 mRNA produced from unaffected cells without any treatment. The decrease in FMR1 mRNA levels at higher nicotinamide and splitomicin concentrations seen in the normal cells (GM02168) was not significant by Students T-test. However, while the effect of 300 µM splitomicin on GM06897 was significant (p = 0.0016), some inhibition of FMR1 mRNA levels was seen at 700 µM such that FMR1 mRNA levels were not significantly different in untreated and splitomicin treated cells (p = 0.49). This inhibition was not seen with other cells and may reflect “off-target” effects of splitomicin on other genes/proteins in these cells.
    Figure Legend Snippet: The effect of nicotinamide and splitomicin on FMR1 gene expression in unaffected and FXS cell lines. (A). Lymphoblastoid cells from an unaffected individual (GM02168), individuals with FXS (GM06897 and GM03200B) treated with the indicated concentrations of nicotinamide. (B and C) Lymphoblastoid cells from an unaffected individual (GM02168), individuals with FXS (GM06897, GM03200B, GM09145 and GM04025) treated with the indicated concentrations of splitomicin. (D) FXS fibroblasts (GM05131 and GM05848) treated with 700 µM splitomicin. FMR1 mRNA levels were measured by real time PCR using Taqman primer-probe mixes. The FMR1 expression in patient cells was plotted as a percentage of the FMR1 mRNA produced from unaffected cells without any treatment. The decrease in FMR1 mRNA levels at higher nicotinamide and splitomicin concentrations seen in the normal cells (GM02168) was not significant by Students T-test. However, while the effect of 300 µM splitomicin on GM06897 was significant (p = 0.0016), some inhibition of FMR1 mRNA levels was seen at 700 µM such that FMR1 mRNA levels were not significantly different in untreated and splitomicin treated cells (p = 0.49). This inhibition was not seen with other cells and may reflect “off-target” effects of splitomicin on other genes/proteins in these cells.

    Techniques Used: Expressing, Real-time Polymerase Chain Reaction, Produced, Inhibition

    9) Product Images from "Interference in transcription of overexpressed genes by promoter-proximal downstream sequences"

    Article Title: Interference in transcription of overexpressed genes by promoter-proximal downstream sequences

    Journal: Scientific Reports

    doi: 10.1038/srep30735

    Nuclear pathways are responsible for the reduced ectopic overexpression of AGO3 and AGO4 mRNAs in human cells. ( A ) Schematic representation of the experimental procedure of U2OS cells fractionation into nuclear and cytoplasmic fractions after transfection with recombinant constructs. ( B ) ( left ) TaqMan qRT-PCR analysis demonstrating relative overexpression of recombinant Argonaute transcripts in cytoplasmic and nuclear fractions after transfection of U2OS cells with pAGO(1–4)LS-nk constructs. The qPCR data is presented as mRNA levels relative to cells transfected with AGO1 encoding plasmids, and normalized on the NeoR mRNA levels in each sample. ( right ) Western immunoblotting demonstrating the absence of cytoplasmic GAPDH protein in nuclear cell fractions and nuclear LaminB protein in cytoplasmic fractions. ( C ) The amounts of AGO1, AGO2, AGO3, AGO4 and NeoR recombinant transcripts in the cytoplasm (left) and nuclear (right) fractions in pAGO(1–4)LS-nk transfected U2OS cells after treatment with actinomycin D for 6 hours (relative to cells treated with DMSO). The qRT-PCR data is presented as mRNA levels for each transcript type relative to cells treated with DMSO, and normalized on the levels of spiked-in synthetic cel-miR-39 control. Note, the half-lives of all transcripts are similar in both cytoplasm and the nuclei.
    Figure Legend Snippet: Nuclear pathways are responsible for the reduced ectopic overexpression of AGO3 and AGO4 mRNAs in human cells. ( A ) Schematic representation of the experimental procedure of U2OS cells fractionation into nuclear and cytoplasmic fractions after transfection with recombinant constructs. ( B ) ( left ) TaqMan qRT-PCR analysis demonstrating relative overexpression of recombinant Argonaute transcripts in cytoplasmic and nuclear fractions after transfection of U2OS cells with pAGO(1–4)LS-nk constructs. The qPCR data is presented as mRNA levels relative to cells transfected with AGO1 encoding plasmids, and normalized on the NeoR mRNA levels in each sample. ( right ) Western immunoblotting demonstrating the absence of cytoplasmic GAPDH protein in nuclear cell fractions and nuclear LaminB protein in cytoplasmic fractions. ( C ) The amounts of AGO1, AGO2, AGO3, AGO4 and NeoR recombinant transcripts in the cytoplasm (left) and nuclear (right) fractions in pAGO(1–4)LS-nk transfected U2OS cells after treatment with actinomycin D for 6 hours (relative to cells treated with DMSO). The qRT-PCR data is presented as mRNA levels for each transcript type relative to cells treated with DMSO, and normalized on the levels of spiked-in synthetic cel-miR-39 control. Note, the half-lives of all transcripts are similar in both cytoplasm and the nuclei.

    Techniques Used: Over Expression, Fractionation, Transfection, Recombinant, Construct, Quantitative RT-PCR, Real-time Polymerase Chain Reaction, Western Blot

    The impact of promoter proximal downstream sequences on transcription is strongly dependent on promoter strength. ( A ) Structure of recombinant construct used for overexpression of FLAG-AGO1 transcript under eCMV, CMV, EF1α + e1, UBC + e1, PGK, TK, EF1α + e1 + i1 and UBC + e1 + i1 promoters and qRT-PCR analysis of recombinant FLAG-AGO1 transcripts generated from those plasmids in U2OS cells 24 hour after transfection. Data is presented as a graph combining relative overexpression efficacy of transcripts from plasmids with eCMV promoter (taken as 100%) vs. transcripts overexpressed from other promoters. Each bar represents mean + S.D of three independent replicates. ( B ) Structure of recombinant constructs used for overexpression of FLAG-AGO1, FLAG-AGO2, FLAG-AGO3 and FLAG-AGO4 transcripts under EF1α + e1, UBC + e1, EF1α + e1 + i1, UBC + e1 + i1, PGK and TK promoters with indicated sizes of exon1 (e1) and intron1 (i1) and a number of Sp1, Ap1 and YY1 binding motifs within the introns. ( C ) TaqMan qPCR analysis of recombinant mRNAs generated from intron-free EF1α + e1, UBC + e1, PGK and TK promoters in U2OS cells 24 h after transfection. ( D ) TaqMan qPCR analysis of recombinant mRNAs generated from intron1 containing promoters EF1α + e1 + i1, UBC + e1 + i1 in U2OS cells 24 h after transfection. All qPCR data is presented as mRNA levels relative to cells transfected with AGO1 encoding plasmids, and normalized on the NeoR mRNA levels for each transfection. Each bar represents mean + S.D of three independent transfections.
    Figure Legend Snippet: The impact of promoter proximal downstream sequences on transcription is strongly dependent on promoter strength. ( A ) Structure of recombinant construct used for overexpression of FLAG-AGO1 transcript under eCMV, CMV, EF1α + e1, UBC + e1, PGK, TK, EF1α + e1 + i1 and UBC + e1 + i1 promoters and qRT-PCR analysis of recombinant FLAG-AGO1 transcripts generated from those plasmids in U2OS cells 24 hour after transfection. Data is presented as a graph combining relative overexpression efficacy of transcripts from plasmids with eCMV promoter (taken as 100%) vs. transcripts overexpressed from other promoters. Each bar represents mean + S.D of three independent replicates. ( B ) Structure of recombinant constructs used for overexpression of FLAG-AGO1, FLAG-AGO2, FLAG-AGO3 and FLAG-AGO4 transcripts under EF1α + e1, UBC + e1, EF1α + e1 + i1, UBC + e1 + i1, PGK and TK promoters with indicated sizes of exon1 (e1) and intron1 (i1) and a number of Sp1, Ap1 and YY1 binding motifs within the introns. ( C ) TaqMan qPCR analysis of recombinant mRNAs generated from intron-free EF1α + e1, UBC + e1, PGK and TK promoters in U2OS cells 24 h after transfection. ( D ) TaqMan qPCR analysis of recombinant mRNAs generated from intron1 containing promoters EF1α + e1 + i1, UBC + e1 + i1 in U2OS cells 24 h after transfection. All qPCR data is presented as mRNA levels relative to cells transfected with AGO1 encoding plasmids, and normalized on the NeoR mRNA levels for each transfection. Each bar represents mean + S.D of three independent transfections.

    Techniques Used: Recombinant, Construct, Over Expression, Quantitative RT-PCR, Generated, Transfection, Binding Assay, Real-time Polymerase Chain Reaction

    The distance of AGO3 and AGO4 coding sequences to the CMV promoter is critical for their expression in human cells. ( A ) ( Left ): Structure of pAGO(1–4)LS-nk, pAGO(1–4)LS-nk-ES and pAGO(1–4)LS-nk-EL used for transient overexpression of AGO coding regions containing either short 200 bp or full-length 720 bp EGFP gene (without the initiating ATG codon) respectively upstream. ( Right ): TaqMan qRT-PCR analysis of recombinant mRNAs generated from these plasmids in U2OS cells 24 h after transfection. ( B ) ( Left ): Structure of pAGO(1–4)LUL containing full-length 1652 bp luciferase gene (without the initiating ATG codon) upstream the AGO coding sequences, and pAGO(1–4)LL plasmids containing the same 1652 bp luciferase gene fragment downstream the AGO coding sequences. ( Right ): TaqMan qRT-PCR analysis of recombinant mRNAs generated from these plasmids in U2OS cells 24 h after transfection. The location of luciferase (LUC) and Argonaute-specific (AGO) TaqMan qPCR assays used is indicated on the corresponding plasmid map. All qPCR data is presented as mRNA levels relative to cells transfected with AGO1 encoding plasmids, and normalized on the NeoR mRNA levels for each transfection. Each bar represents mean + S.D of three independent transfections. ( C ) ( Left ): Structure of the parental pAGO(1–4)LS-wt and the derivative pAGO(1–4)LS-wt-ELnoATG construct containing the 714 bp EGFP cDNA deprived from all ATG codons upstream the AGO coding regions. ( Right ): Western immunoblot performed with anti-FLAG and anti-β-actin antibody showing FLAG-AGO1, FLAG-AGO2, FLAG-AGO3, FLAG-AGO4 and actin proteins expression in U2OS cells 24 h after transfection with pAGO(1–4)LS-wt and pAGO(1–4)LS-wt-ELnoATG.
    Figure Legend Snippet: The distance of AGO3 and AGO4 coding sequences to the CMV promoter is critical for their expression in human cells. ( A ) ( Left ): Structure of pAGO(1–4)LS-nk, pAGO(1–4)LS-nk-ES and pAGO(1–4)LS-nk-EL used for transient overexpression of AGO coding regions containing either short 200 bp or full-length 720 bp EGFP gene (without the initiating ATG codon) respectively upstream. ( Right ): TaqMan qRT-PCR analysis of recombinant mRNAs generated from these plasmids in U2OS cells 24 h after transfection. ( B ) ( Left ): Structure of pAGO(1–4)LUL containing full-length 1652 bp luciferase gene (without the initiating ATG codon) upstream the AGO coding sequences, and pAGO(1–4)LL plasmids containing the same 1652 bp luciferase gene fragment downstream the AGO coding sequences. ( Right ): TaqMan qRT-PCR analysis of recombinant mRNAs generated from these plasmids in U2OS cells 24 h after transfection. The location of luciferase (LUC) and Argonaute-specific (AGO) TaqMan qPCR assays used is indicated on the corresponding plasmid map. All qPCR data is presented as mRNA levels relative to cells transfected with AGO1 encoding plasmids, and normalized on the NeoR mRNA levels for each transfection. Each bar represents mean + S.D of three independent transfections. ( C ) ( Left ): Structure of the parental pAGO(1–4)LS-wt and the derivative pAGO(1–4)LS-wt-ELnoATG construct containing the 714 bp EGFP cDNA deprived from all ATG codons upstream the AGO coding regions. ( Right ): Western immunoblot performed with anti-FLAG and anti-β-actin antibody showing FLAG-AGO1, FLAG-AGO2, FLAG-AGO3, FLAG-AGO4 and actin proteins expression in U2OS cells 24 h after transfection with pAGO(1–4)LS-wt and pAGO(1–4)LS-wt-ELnoATG.

    Techniques Used: Expressing, Over Expression, Quantitative RT-PCR, Recombinant, Generated, Transfection, Luciferase, Real-time Polymerase Chain Reaction, Plasmid Preparation, Construct, Western Blot

    Different overexpression efficiency of human Argonaute coding sequences. ( A ) Structure of pAGO1LS-wt, pAGO2LS-wt, pAGO3LS-wt and pAGO4LS-wt used for transient overexpression of recombinant human Argonautes coding regions containing N-terminal FLAG-tag. The location of the luciferase TaqMan qPCR probe (LUC) is indicated on the plasmid map. ( B ) Structure of pAGO1LS-nk, pAGO2LS-nk, pAGO3LS-nk and pAGO4LS-nk encoding protein synthesis-impaired AGO cDNAs (lacking Kozak sequences and the first 2 nucleotides in the starting ATG codons). The location of the 5′-end and 3′-end (LUC) TaqMan qPCR probes is indicated on the plasmid map. TaqMan qRT-PCR analysis was used to estimate the relative overexpression of recombinant Argonaute transcripts generated from pAGO(1–4)LS-wt ( C ) and pAGO(1–4)LS-nk plasmids ( D ) in U2OS cells 24 h after transient transfection. The qPCR data is presented as mRNA levels relative to cells transfected with AGO1 encoding plasmids, and normalized on the NeoR mRNA levels in each sample. Each bar represents mean + S.D of three independent transfections. (E ) Western immunoblotting demonstrating expression of FLAG-AGO1, FLAG-AGO2, FLAG-AGO3, FLAG-AGO4, EGFP and β-actin proteins in U2OS cells 24 h after transfection with pAGO1LS-wt, pAGO2LS-wt, pAGO3LS-wt and pAGO4LS-wt vectors mixed with equal amount of pEFGP-C1 plasmid. ( F) Western immunoblotting performed with anti-FLAG and anti-AGO1 antibodies demonstrating the absence of recombinant AGO1 protein production in U2OS cells after transfection with pAGO1LS-nk plasmid, in contrast to cells transfected with pAGO1LS-wt.
    Figure Legend Snippet: Different overexpression efficiency of human Argonaute coding sequences. ( A ) Structure of pAGO1LS-wt, pAGO2LS-wt, pAGO3LS-wt and pAGO4LS-wt used for transient overexpression of recombinant human Argonautes coding regions containing N-terminal FLAG-tag. The location of the luciferase TaqMan qPCR probe (LUC) is indicated on the plasmid map. ( B ) Structure of pAGO1LS-nk, pAGO2LS-nk, pAGO3LS-nk and pAGO4LS-nk encoding protein synthesis-impaired AGO cDNAs (lacking Kozak sequences and the first 2 nucleotides in the starting ATG codons). The location of the 5′-end and 3′-end (LUC) TaqMan qPCR probes is indicated on the plasmid map. TaqMan qRT-PCR analysis was used to estimate the relative overexpression of recombinant Argonaute transcripts generated from pAGO(1–4)LS-wt ( C ) and pAGO(1–4)LS-nk plasmids ( D ) in U2OS cells 24 h after transient transfection. The qPCR data is presented as mRNA levels relative to cells transfected with AGO1 encoding plasmids, and normalized on the NeoR mRNA levels in each sample. Each bar represents mean + S.D of three independent transfections. (E ) Western immunoblotting demonstrating expression of FLAG-AGO1, FLAG-AGO2, FLAG-AGO3, FLAG-AGO4, EGFP and β-actin proteins in U2OS cells 24 h after transfection with pAGO1LS-wt, pAGO2LS-wt, pAGO3LS-wt and pAGO4LS-wt vectors mixed with equal amount of pEFGP-C1 plasmid. ( F) Western immunoblotting performed with anti-FLAG and anti-AGO1 antibodies demonstrating the absence of recombinant AGO1 protein production in U2OS cells after transfection with pAGO1LS-nk plasmid, in contrast to cells transfected with pAGO1LS-wt.

    Techniques Used: Over Expression, Recombinant, FLAG-tag, Luciferase, Real-time Polymerase Chain Reaction, Plasmid Preparation, Quantitative RT-PCR, Generated, Transfection, Western Blot, Expressing

    10) Product Images from "Blocking the Maturation of OncomiRNAs Using pri-miRNA-17∼92 Aptamer in Retinoblastoma"

    Article Title: Blocking the Maturation of OncomiRNAs Using pri-miRNA-17∼92 Aptamer in Retinoblastoma

    Journal: Nucleic Acid Therapeutics

    doi: 10.1089/nat.2014.0507

    Primary microRNA (pri-miRNA) aptamer inhibits mature miRNA formation. (A) Relative expression levels of mature mir-17, mir-18a, and mir-19b using TaqMan-based qualitative PCR and normalized to untreated control sample with RNU6B as endogenous control
    Figure Legend Snippet: Primary microRNA (pri-miRNA) aptamer inhibits mature miRNA formation. (A) Relative expression levels of mature mir-17, mir-18a, and mir-19b using TaqMan-based qualitative PCR and normalized to untreated control sample with RNU6B as endogenous control

    Techniques Used: Expressing, Polymerase Chain Reaction

    11) Product Images from "Altered expression of neuropeptides in FoxG1-null heterozygous mutant mice"

    Article Title: Altered expression of neuropeptides in FoxG1-null heterozygous mutant mice

    Journal: European Journal of Human Genetics

    doi: 10.1038/ejhg.2015.79

    Relative quantification of mRNA levels of Nnat and Mef2c in silenced neurons assessed by qRT-PCR using commercial Taqman probes. Analyses were performed in triplicate and data are reported as mean+SEM.
    Figure Legend Snippet: Relative quantification of mRNA levels of Nnat and Mef2c in silenced neurons assessed by qRT-PCR using commercial Taqman probes. Analyses were performed in triplicate and data are reported as mean+SEM.

    Techniques Used: Quantitative RT-PCR

    ( a ) Relative quantification of mRNA levels of OXT, AVP, NNAT and MEF2C genes assessed by qRT-PCR using commercial Taqman probes. Analyses were performed in triplicate on the same tissues used for cDNA microarray experiments and data are reported as mean±SEM, * P
    Figure Legend Snippet: ( a ) Relative quantification of mRNA levels of OXT, AVP, NNAT and MEF2C genes assessed by qRT-PCR using commercial Taqman probes. Analyses were performed in triplicate on the same tissues used for cDNA microarray experiments and data are reported as mean±SEM, * P

    Techniques Used: Quantitative RT-PCR, Microarray

    12) Product Images from "ZnT3 mRNA levels are reduced in Alzheimer's disease post-mortem brain"

    Article Title: ZnT3 mRNA levels are reduced in Alzheimer's disease post-mortem brain

    Journal: Molecular Neurodegeneration

    doi: 10.1186/1750-1326-4-53

    ZnT3 efficiency plot . Quadruplicate ZnT3 qPCR analyses were carried out using the indicated dilutions of a cDNA pool, derived as described in the Methods section. Mean Ct values ± SD are presented for each dilution where the assay signal rose above the detection threshold. PCR reaction efficiency for the ZnT3 TaqMan assay (85%) was calculated from the slope of the line as described in the Methods section.
    Figure Legend Snippet: ZnT3 efficiency plot . Quadruplicate ZnT3 qPCR analyses were carried out using the indicated dilutions of a cDNA pool, derived as described in the Methods section. Mean Ct values ± SD are presented for each dilution where the assay signal rose above the detection threshold. PCR reaction efficiency for the ZnT3 TaqMan assay (85%) was calculated from the slope of the line as described in the Methods section.

    Techniques Used: Real-time Polymerase Chain Reaction, Derivative Assay, Polymerase Chain Reaction, TaqMan Assay

    13) Product Images from "Ropinirole alters gene expression profiles in SH-SY5Y cells: a whole genome microarray study"

    Article Title: Ropinirole alters gene expression profiles in SH-SY5Y cells: a whole genome microarray study

    Journal: Brazilian Journal of Medical and Biological Research

    doi: 10.1590/1414-431X20154857

    TaqMan¯ real-time PCR confirmation of microarray data in SH-SY5Y cells. CALM3 , EPS15 , RIPK5 , and PIK3C2B underwent TaqMan real-time PCR in SH-SY5Y cells. The y-axis represents the fold-change in expression after ROP treatment, and microarray and TaqMan data are plotted on the x-axis. There were no significant differences between the microarray and TaqMan data (P > 0.05; Student's t- test).
    Figure Legend Snippet: TaqMan¯ real-time PCR confirmation of microarray data in SH-SY5Y cells. CALM3 , EPS15 , RIPK5 , and PIK3C2B underwent TaqMan real-time PCR in SH-SY5Y cells. The y-axis represents the fold-change in expression after ROP treatment, and microarray and TaqMan data are plotted on the x-axis. There were no significant differences between the microarray and TaqMan data (P > 0.05; Student's t- test).

    Techniques Used: Real-time Polymerase Chain Reaction, Microarray, Expressing

    Validation of microarray data in HeLa cells. A , CALM3 , EPS15 , RIPK5 , and PIK3C2B underwent TaqMan ¯ real-time PCR in HeLa cells. The y-axis represents the fold-change in expression after ROP treatment, and microarray and TaqMan data are plotted on the x-axis. *P
    Figure Legend Snippet: Validation of microarray data in HeLa cells. A , CALM3 , EPS15 , RIPK5 , and PIK3C2B underwent TaqMan ¯ real-time PCR in HeLa cells. The y-axis represents the fold-change in expression after ROP treatment, and microarray and TaqMan data are plotted on the x-axis. *P

    Techniques Used: Microarray, Real-time Polymerase Chain Reaction, Expressing

    14) Product Images from "An Engineered Galactosylceramidase Construct Improves AAV Gene Therapy for Krabbe Disease in Twitcher Mice"

    Article Title: An Engineered Galactosylceramidase Construct Improves AAV Gene Therapy for Krabbe Disease in Twitcher Mice

    Journal: Human Gene Therapy

    doi: 10.1089/hum.2019.008

    Bodywide evaluation of the expression of the engineered galactosylceramidase and the biodistribution of the AAV9 vector. (A) Western blot evaluation of the engineered galactosylceramidase from three AAV-treated twitcher mice. Flag tag marks the location of the engineered galactosylceramidase (81 kDa). Alpha-tubulin (50 kDa) is used as the loading control. (B) TaqMan PCR quantification of the AAV9 genome copy number in various tissues. Gas, gastrocnemius muscle; TA, tibialis anterior muscle.
    Figure Legend Snippet: Bodywide evaluation of the expression of the engineered galactosylceramidase and the biodistribution of the AAV9 vector. (A) Western blot evaluation of the engineered galactosylceramidase from three AAV-treated twitcher mice. Flag tag marks the location of the engineered galactosylceramidase (81 kDa). Alpha-tubulin (50 kDa) is used as the loading control. (B) TaqMan PCR quantification of the AAV9 genome copy number in various tissues. Gas, gastrocnemius muscle; TA, tibialis anterior muscle.

    Techniques Used: Expressing, Plasmid Preparation, Western Blot, Mouse Assay, FLAG-tag, Polymerase Chain Reaction

    15) Product Images from "Quantitative Gene Expression Analysis in Microdissected Archival Formalin-Fixed and Paraffin-Embedded Tumor Tissue"

    Article Title: Quantitative Gene Expression Analysis in Microdissected Archival Formalin-Fixed and Paraffin-Embedded Tumor Tissue

    Journal: The American Journal of Pathology

    doi:

    Quantitative gene expression analysis of EGF-R mRNA measured by real-time TaqMan QRT-PCR in matching frozen and formalin-fixed, paraffin-embedded HT29 human tumor xenografts. A: Five-μm section of a formalin-fixed, paraffin-embedded HT29 tumor xenograft stained with H E, demonstrating the homogenous tumor histology. Original magnification, ×400. B: Serial dilutions of total RNA extracted from matching frozen and formalin-fixed, paraffin-embedded tissue samples from a HT29 tumor xenograft were subjected to 45 cycles of real-time TaqMan QRT-PCR of the EGF-R sequence. Shown are the PCR products on a 3% agarose gel after electrophoresis and ethidium bromide staining. Lane M: MSP I -digested pUC molecular weight DNA. Lanes 1 and 7: 50 ng RNA. Lanes 2 and 8: 10 ng RNA. Lanes 3 and 9: 2 ng RNA. Lanes 4 and 10: 0.4 ng RNA. Lanes 5 and 11: 0.08 ng RNA. Lanes 6 and 12: 16 pg RNA. No signals were generated using no-template control reactions ( Lane 13 ) or genomic DNA ( Lane 14 ). The arrow indicates the 93-bp EGF-R amplification product. C: The logarithm of the input RNA amount of the same samples is plotted versus the threshold cycle (Ct) monitored during real-time TaqMan QRT-PCR. Amplification efficiency of the EGF-R gene in matching frozen and formalin-fixed, paraffin-embedded tissue samples from HT29 tumor xenografts is comparable, as indicated by similar slopes of the regression lines. All points represent the mean of duplicate PCR amplifications, but error bars are too small to be visible.
    Figure Legend Snippet: Quantitative gene expression analysis of EGF-R mRNA measured by real-time TaqMan QRT-PCR in matching frozen and formalin-fixed, paraffin-embedded HT29 human tumor xenografts. A: Five-μm section of a formalin-fixed, paraffin-embedded HT29 tumor xenograft stained with H E, demonstrating the homogenous tumor histology. Original magnification, ×400. B: Serial dilutions of total RNA extracted from matching frozen and formalin-fixed, paraffin-embedded tissue samples from a HT29 tumor xenograft were subjected to 45 cycles of real-time TaqMan QRT-PCR of the EGF-R sequence. Shown are the PCR products on a 3% agarose gel after electrophoresis and ethidium bromide staining. Lane M: MSP I -digested pUC molecular weight DNA. Lanes 1 and 7: 50 ng RNA. Lanes 2 and 8: 10 ng RNA. Lanes 3 and 9: 2 ng RNA. Lanes 4 and 10: 0.4 ng RNA. Lanes 5 and 11: 0.08 ng RNA. Lanes 6 and 12: 16 pg RNA. No signals were generated using no-template control reactions ( Lane 13 ) or genomic DNA ( Lane 14 ). The arrow indicates the 93-bp EGF-R amplification product. C: The logarithm of the input RNA amount of the same samples is plotted versus the threshold cycle (Ct) monitored during real-time TaqMan QRT-PCR. Amplification efficiency of the EGF-R gene in matching frozen and formalin-fixed, paraffin-embedded tissue samples from HT29 tumor xenografts is comparable, as indicated by similar slopes of the regression lines. All points represent the mean of duplicate PCR amplifications, but error bars are too small to be visible.

    Techniques Used: Expressing, Quantitative RT-PCR, Formalin-fixed Paraffin-Embedded, Staining, Sequencing, Polymerase Chain Reaction, Agarose Gel Electrophoresis, Electrophoresis, Molecular Weight, Generated, Amplification

    Influence of the formalin fixation procedure on quantitative gene expression analysis by TaqMan QRT-PCR. Liver and uterus with leiomyoma tissue samples that had been fixed for 20 hours were cut in sequential sections of 1 cm to a depth of 3 cm (liver) or 6 cm (uterus with leiomyoma). Quantitation of EGF-R , HER-2/neu , FGF-R4 , p21/WAF1/Cip1 , MDM2 , and HPRT (liver) and p21/WAF1/Cip1 and HPRT (uterus and leiomyoma) was determined relative to PGK as a housekeeping gene in single 5-μm sections of the sequential blocks. Change in gene expression of the six different genes is shown relative to a 5-μm section at 1-cm depth for liver ( A ) and uterus with myometrium and leiomyoma ( B ). Shown are the results of two different measurements, each run in duplicate ±SEM. ( C ) Absolute Ct values for PGK and HPRT that were used for quantitation of relative expression of the mRNAs.
    Figure Legend Snippet: Influence of the formalin fixation procedure on quantitative gene expression analysis by TaqMan QRT-PCR. Liver and uterus with leiomyoma tissue samples that had been fixed for 20 hours were cut in sequential sections of 1 cm to a depth of 3 cm (liver) or 6 cm (uterus with leiomyoma). Quantitation of EGF-R , HER-2/neu , FGF-R4 , p21/WAF1/Cip1 , MDM2 , and HPRT (liver) and p21/WAF1/Cip1 and HPRT (uterus and leiomyoma) was determined relative to PGK as a housekeeping gene in single 5-μm sections of the sequential blocks. Change in gene expression of the six different genes is shown relative to a 5-μm section at 1-cm depth for liver ( A ) and uterus with myometrium and leiomyoma ( B ). Shown are the results of two different measurements, each run in duplicate ±SEM. ( C ) Absolute Ct values for PGK and HPRT that were used for quantitation of relative expression of the mRNAs.

    Techniques Used: Expressing, Quantitative RT-PCR, Quantitation Assay

    Quantitative determination of gene expression measured by real-time TaqMan QRT-PCR in matching frozen and formalin-fixed, paraffin-embedded HT29 and A431 human tumor xenografts. Levels of EGF-R , HER-2/neu , FGF-R4 , p21/WAF1/Cip1 , MDM2 , and PGK mRNAs were determined by QRT-PCR and all measurements are shown relative to the expression levels of the PGK housekeeping gene. Results shown are the mean of three independent RNA isolations from single consecutive 5-μm sections ±SEM ( n = 3).
    Figure Legend Snippet: Quantitative determination of gene expression measured by real-time TaqMan QRT-PCR in matching frozen and formalin-fixed, paraffin-embedded HT29 and A431 human tumor xenografts. Levels of EGF-R , HER-2/neu , FGF-R4 , p21/WAF1/Cip1 , MDM2 , and PGK mRNAs were determined by QRT-PCR and all measurements are shown relative to the expression levels of the PGK housekeeping gene. Results shown are the mean of three independent RNA isolations from single consecutive 5-μm sections ±SEM ( n = 3).

    Techniques Used: Expressing, Quantitative RT-PCR, Formalin-fixed Paraffin-Embedded

    Effect of amplicon size on quantitative gene expression analysis by TaqMan QRT-PCR in matched frozen and formalin-fixed, paraffin-embedded tissue samples from A431 xenograft tumors. Seven primer/probe pairs for QRT-PCR were tested that amplify 66-, 98-, 122-, 158-, 182-, 319-, and 374-base-long portions of p21/WAF1/Cip1 mRNA. The same forward primer and TaqMan probe were used in each case. A: Absolute Ct values for the seven primer pair combinations. Best results are obtained in FFPE tissue with QRT-PCR primer pairs spanning fragments
    Figure Legend Snippet: Effect of amplicon size on quantitative gene expression analysis by TaqMan QRT-PCR in matched frozen and formalin-fixed, paraffin-embedded tissue samples from A431 xenograft tumors. Seven primer/probe pairs for QRT-PCR were tested that amplify 66-, 98-, 122-, 158-, 182-, 319-, and 374-base-long portions of p21/WAF1/Cip1 mRNA. The same forward primer and TaqMan probe were used in each case. A: Absolute Ct values for the seven primer pair combinations. Best results are obtained in FFPE tissue with QRT-PCR primer pairs spanning fragments

    Techniques Used: Amplification, Expressing, Quantitative RT-PCR, Formalin-fixed Paraffin-Embedded

    Specificity of the TaqMan QRT-PCR amplification. A: Real-time RT-PCR amplification plot of TBP mRNA measured in formalin-fixed, paraffin-embedded liver, myometrium and leiomyoma tissues, and a prostate cancer specimen. mRNA-specific signals are detectable in all four tissue types. B: Real-time RT-PCR amplification plot of PSA mRNA in the same tissues as indicated above, showing the specific detection of the PSA mRNA transcript only in the prostate cancer specimen. C: The same PCR products subjected to 3% agarose gel electrophoresis and ethidium bromide staining. Lane M: Molecular Weight Marker VIII (Roche Molecular Biochemicals). The arrow indicates the 110-bp fragment of the Molecular Weight Marker VIII.
    Figure Legend Snippet: Specificity of the TaqMan QRT-PCR amplification. A: Real-time RT-PCR amplification plot of TBP mRNA measured in formalin-fixed, paraffin-embedded liver, myometrium and leiomyoma tissues, and a prostate cancer specimen. mRNA-specific signals are detectable in all four tissue types. B: Real-time RT-PCR amplification plot of PSA mRNA in the same tissues as indicated above, showing the specific detection of the PSA mRNA transcript only in the prostate cancer specimen. C: The same PCR products subjected to 3% agarose gel electrophoresis and ethidium bromide staining. Lane M: Molecular Weight Marker VIII (Roche Molecular Biochemicals). The arrow indicates the 110-bp fragment of the Molecular Weight Marker VIII.

    Techniques Used: Quantitative RT-PCR, Amplification, Formalin-fixed Paraffin-Embedded, Polymerase Chain Reaction, Agarose Gel Electrophoresis, Staining, Molecular Weight, Marker

    16) Product Images from "The Rcs Phosphorelay Is a Cell Envelope Stress Response Activated by Peptidoglycan Stress and Contributes to Intrinsic Antibiotic Resistance ▿The Rcs Phosphorelay Is a Cell Envelope Stress Response Activated by Peptidoglycan Stress and Contributes to Intrinsic Antibiotic Resistance ▿ †"

    Article Title: The Rcs Phosphorelay Is a Cell Envelope Stress Response Activated by Peptidoglycan Stress and Contributes to Intrinsic Antibiotic Resistance ▿The Rcs Phosphorelay Is a Cell Envelope Stress Response Activated by Peptidoglycan Stress and Contributes to Intrinsic Antibiotic Resistance ▿ †

    Journal: Journal of Bacteriology

    doi: 10.1128/JB.01740-07

    TaqMan quantitative real-time PCR.
    Figure Legend Snippet: TaqMan quantitative real-time PCR.

    Techniques Used: Real-time Polymerase Chain Reaction

    17) Product Images from "Sensitive and specific miRNA detection method using SplintR Ligase"

    Article Title: Sensitive and specific miRNA detection method using SplintR Ligase

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkw399

    Comparison of SplintR ligation method to TaqMan assay for detection of miR-122 in rat liver RNA. Three different concentrations of rat liver total RNA were used; 1 ng (green), 0.2 ng (blue), 0.04 ng/μ (red) and no rat liver RNA (black). ( A ) This panel shows the qPCR traces for the SplintR method described in Figure 2 . The ligated probes were amplified by PCR and detected with a double quenched miR-122 specific DNA probe. ( B ) TaqMan detection method for miR-122 used a DNA hairpin complementary to the 3′ end of the miRNA to prime cDNA synthesis with reverse transcriptase. The amplified product is detected by cleavage of a TaqMan probe specific for miR-122 (miR-122 sqp). The sequences of the probes and protocols for amplification and detection are described in Materials and Methods.
    Figure Legend Snippet: Comparison of SplintR ligation method to TaqMan assay for detection of miR-122 in rat liver RNA. Three different concentrations of rat liver total RNA were used; 1 ng (green), 0.2 ng (blue), 0.04 ng/μ (red) and no rat liver RNA (black). ( A ) This panel shows the qPCR traces for the SplintR method described in Figure 2 . The ligated probes were amplified by PCR and detected with a double quenched miR-122 specific DNA probe. ( B ) TaqMan detection method for miR-122 used a DNA hairpin complementary to the 3′ end of the miRNA to prime cDNA synthesis with reverse transcriptase. The amplified product is detected by cleavage of a TaqMan probe specific for miR-122 (miR-122 sqp). The sequences of the probes and protocols for amplification and detection are described in Materials and Methods.

    Techniques Used: Ligation, TaqMan Assay, Real-time Polymerase Chain Reaction, Amplification, Polymerase Chain Reaction

    18) Product Images from "Frequent Detection of Human Coronaviruses in Clinical Specimens from Patients with Respiratory Tract Infection by Use of a Novel Real-Time Reverse-Transcriptase Polymerase Chain Reaction"

    Article Title: Frequent Detection of Human Coronaviruses in Clinical Specimens from Patients with Respiratory Tract Infection by Use of a Novel Real-Time Reverse-Transcriptase Polymerase Chain Reaction

    Journal: The Journal of Infectious Diseases

    doi: 10.1086/381207

    Longitudinal follow-up of 5 patients with either human coronavirus OC43 or 229E infection. Quantitative analysis was performed by use of the multiplex Taqman-based polymerase chain reaction. The quantity is expressed on the Y -axis as relative units (RU). RU = 2 36-threshold cycle
    Figure Legend Snippet: Longitudinal follow-up of 5 patients with either human coronavirus OC43 or 229E infection. Quantitative analysis was performed by use of the multiplex Taqman-based polymerase chain reaction. The quantity is expressed on the Y -axis as relative units (RU). RU = 2 36-threshold cycle

    Techniques Used: Infection, Multiplex Assay, Polymerase Chain Reaction

    Virus quantity expressed as relative units (RU) of human coronavirus (HCoV) that could be detected in the clinical specimens ( n = 14). ◯, Clinical specimens tested by Taqman-based real-time polymerase chain reaction (PCR) only; □, clinical specimens tested by both the in-house nested PCR and the Taqman-based real-time PCR.
    Figure Legend Snippet: Virus quantity expressed as relative units (RU) of human coronavirus (HCoV) that could be detected in the clinical specimens ( n = 14). ◯, Clinical specimens tested by Taqman-based real-time polymerase chain reaction (PCR) only; □, clinical specimens tested by both the in-house nested PCR and the Taqman-based real-time PCR.

    Techniques Used: Real-time Polymerase Chain Reaction, Polymerase Chain Reaction, Nested PCR

    19) Product Images from "Neutrophil Chemokines Secreted by Tumor Cells Mount a Lung Antimetastatic Response during Renal Cell Carcinoma Progression"

    Article Title: Neutrophil Chemokines Secreted by Tumor Cells Mount a Lung Antimetastatic Response during Renal Cell Carcinoma Progression

    Journal: Oncogene

    doi: 10.1038/onc.2012.201

    CXCL chemokines expression decreased during RCC metastatic progression (A) Genes showing 5-fold or greater alteration in expression in the SN12C cell line compared to the LM2 cell line. (B) Expression of IL8 + CXCL5 in a panel of RCC cell lines isolated from primary or metastatic tumors determined by Q-PCR. Error bars represent STDEV. P-values were obtained using Student’s t-test of comparing primary cells versus metastatic cells. (C) Comparison of CXCL5 DNA copy number in primary and metastatic cell lines using TaqMan copy number assay
    Figure Legend Snippet: CXCL chemokines expression decreased during RCC metastatic progression (A) Genes showing 5-fold or greater alteration in expression in the SN12C cell line compared to the LM2 cell line. (B) Expression of IL8 + CXCL5 in a panel of RCC cell lines isolated from primary or metastatic tumors determined by Q-PCR. Error bars represent STDEV. P-values were obtained using Student’s t-test of comparing primary cells versus metastatic cells. (C) Comparison of CXCL5 DNA copy number in primary and metastatic cell lines using TaqMan copy number assay

    Techniques Used: Expressing, Isolation, Polymerase Chain Reaction, TaqMan Copy Number Assay

    20) Product Images from "Sika deer (Cervus nippon)-specific real-time PCR method to detect fraudulent labelling of meat and meat products"

    Article Title: Sika deer (Cervus nippon)-specific real-time PCR method to detect fraudulent labelling of meat and meat products

    Journal: Scientific Reports

    doi: 10.1038/s41598-018-25299-7

    Results obtained in cross-reactivity tests performed with DNA isolates from 23 animal species with 5 commercial master mixes. ( A ) QuantiTect® Multiplex PCR NoROX Master Mix (Qiagen), ( B ) TaqMan® Universal PCR Master Mix (Applied Biosystems), ( C ) GoTaq® Probe qPCR Master Mix (Promega), ( D ) PerfeCTa® qPCR ToughMix TM , Low ROX TM (Quanta Biosciences) and E) Takyon TM No Rox Probe MasterMix dTTP Blue (Eurogentec).
    Figure Legend Snippet: Results obtained in cross-reactivity tests performed with DNA isolates from 23 animal species with 5 commercial master mixes. ( A ) QuantiTect® Multiplex PCR NoROX Master Mix (Qiagen), ( B ) TaqMan® Universal PCR Master Mix (Applied Biosystems), ( C ) GoTaq® Probe qPCR Master Mix (Promega), ( D ) PerfeCTa® qPCR ToughMix TM , Low ROX TM (Quanta Biosciences) and E) Takyon TM No Rox Probe MasterMix dTTP Blue (Eurogentec).

    Techniques Used: Multiplex Assay, Polymerase Chain Reaction, Real-time Polymerase Chain Reaction

    21) Product Images from "Overexpression of the Cytotoxic T Cell (CT) Carbohydrate Inhibits Muscular Dystrophy in the dyW Mouse Model of Congenital Muscular Dystrophy 1A"

    Article Title: Overexpression of the Cytotoxic T Cell (CT) Carbohydrate Inhibits Muscular Dystrophy in the dyW Mouse Model of Congenital Muscular Dystrophy 1A

    Journal:

    doi: 10.2353/ajpath.2007.060927

    Endogenous Galgt2 gene expression is increased in mdx and dy W /dy W muscle and the Galgt2 transgene is differentially overexpressed in the two disease models. A: Galgt2 gene expression was measured by TaqMan RT-PCR in mdx and dy W /dy W skeletal muscle compared
    Figure Legend Snippet: Endogenous Galgt2 gene expression is increased in mdx and dy W /dy W muscle and the Galgt2 transgene is differentially overexpressed in the two disease models. A: Galgt2 gene expression was measured by TaqMan RT-PCR in mdx and dy W /dy W skeletal muscle compared

    Techniques Used: Expressing, Reverse Transcription Polymerase Chain Reaction

    22) Product Images from "Overexpression of the Cytotoxic T Cell (CT) Carbohydrate Inhibits Muscular Dystrophy in the dyW Mouse Model of Congenital Muscular Dystrophy 1A"

    Article Title: Overexpression of the Cytotoxic T Cell (CT) Carbohydrate Inhibits Muscular Dystrophy in the dyW Mouse Model of Congenital Muscular Dystrophy 1A

    Journal:

    doi: 10.2353/ajpath.2007.060927

    Endogenous Galgt2 gene expression is increased in mdx and dy W /dy W muscle and the Galgt2 transgene is differentially overexpressed in the two disease models. A: Galgt2 gene expression was measured by TaqMan RT-PCR in mdx and dy W /dy W skeletal muscle compared
    Figure Legend Snippet: Endogenous Galgt2 gene expression is increased in mdx and dy W /dy W muscle and the Galgt2 transgene is differentially overexpressed in the two disease models. A: Galgt2 gene expression was measured by TaqMan RT-PCR in mdx and dy W /dy W skeletal muscle compared

    Techniques Used: Expressing, Reverse Transcription Polymerase Chain Reaction

    23) Product Images from "Anti-angiogenic effects of differentiation-inducing factor-1 involving VEGFR-2 expression inhibition independent of the Wnt/?-catenin signaling pathway"

    Article Title: Anti-angiogenic effects of differentiation-inducing factor-1 involving VEGFR-2 expression inhibition independent of the Wnt/?-catenin signaling pathway

    Journal: Molecular Cancer

    doi: 10.1186/1476-4598-9-245

    DIF-1 reduced VEGFR-2 mRNA level and promoter activity . (A) The effects of DIF-1 on the VEGFR-2 mRNA levels. Total RNAs were extracted from HUVECs treated with or without DIF-1 (30 μM) for 24 h. The VEGFR-2 mRNA levels were determined by TaqMan quantitative real-time RT-PCR. Values are mean ± SE of four independent experiments. The asterisk indicates *P
    Figure Legend Snippet: DIF-1 reduced VEGFR-2 mRNA level and promoter activity . (A) The effects of DIF-1 on the VEGFR-2 mRNA levels. Total RNAs were extracted from HUVECs treated with or without DIF-1 (30 μM) for 24 h. The VEGFR-2 mRNA levels were determined by TaqMan quantitative real-time RT-PCR. Values are mean ± SE of four independent experiments. The asterisk indicates *P

    Techniques Used: Activity Assay, Quantitative RT-PCR

    24) Product Images from "Identification of circulating microRNAs as diagnostic biomarkers for use in multiple myeloma"

    Article Title: Identification of circulating microRNAs as diagnostic biomarkers for use in multiple myeloma

    Journal: British Journal of Cancer

    doi: 10.1038/bjc.2012.525

    Comparison of the serum levels of miR-720 ( A ), miR-1308 ( B ) and miR-1246 ( C ) in Normal (N), Normal hospitalised (NH), MGUS (MG) and myeloma (M) groups. Graphs show median level with interquartile range. The Kruskal–Wallis test with Dunn's post test was used to determine the significance of differences between groups. The serum levels were determined using TaqMan miRNA qRT–PCR following RNA extraction. Two technical replicates were performed on two cDNA replicates (four technical replicates total per sample/miRNA combination.
    Figure Legend Snippet: Comparison of the serum levels of miR-720 ( A ), miR-1308 ( B ) and miR-1246 ( C ) in Normal (N), Normal hospitalised (NH), MGUS (MG) and myeloma (M) groups. Graphs show median level with interquartile range. The Kruskal–Wallis test with Dunn's post test was used to determine the significance of differences between groups. The serum levels were determined using TaqMan miRNA qRT–PCR following RNA extraction. Two technical replicates were performed on two cDNA replicates (four technical replicates total per sample/miRNA combination.

    Techniques Used: Quantitative RT-PCR, RNA Extraction

    25) Product Images from "Contribution of Protein p40 to Hypovirus-Mediated Modulation of Fungal Host Phenotype and Viral RNA Accumulation"

    Article Title: Contribution of Protein p40 to Hypovirus-Mediated Modulation of Fungal Host Phenotype and Viral RNA Accumulation

    Journal: Journal of Virology

    doi: 10.1128/JVI.76.15.7747-7759.2002

    (A) Agarose gel electrophoretic analysis of total RNA isolated from C. parasitica colonies transfected with mutant recombinant viruses. Equal amounts (OD, 0.25) of total RNA extracted from uninfected mycelia (lane 7) and mycelia infected with CHV1-EP713 wild-type virus (lane 1) or mutant viruses Δp29 (lane 2), Δp40a (lane 3), Δp40b (lane 4), Δp69a (lane 5), and Δp69b (lane 6) were electrophoresed through a 0.7% agarose gel in the TAE buffer system (40 mM Tris-acetate-1 mM EDTA, pH 7.8) and stained with ethidium bromide. Lane M was loaded in parallel with 1-kb ladder DNA size markers (Gibco-BRL, Gaithersburg, Md.). Relative mobilities of viral dsRNA are indicated. (B) Relative accumulation of viral minus-strand RNA in fungal colonies infected with wild-type CHV1-EP713 and mutant viruses. Total RNA was isolated from mycelia infected with CHV1-EP713 (bar 1) and mutant viruses Δp29 (bar 2), Δp40a (bar 3), Δp40b (bar 4), Δp69a (bar 5), and Δp69b (bar 6) and used for strand-specific cDNA synthesis after denaturation in 90% dimethyl sulfoxide at 65°C. The resulting cDNA was subjected to semiquantitative PCR analysis in a GeneAmp 5700 sequence detection system by using cDNA of 18S rRNA generated in the same RT reaction for normalization. The sequences of primers and TaqMan probes used in the quantification are described in Methods and Materials. Viral minus-strand RNA accumulation levels are reported as percentages of the value for CHV1-EP713-infected colonies, with standard deviations based on three independent measurements indicated by the error bars.
    Figure Legend Snippet: (A) Agarose gel electrophoretic analysis of total RNA isolated from C. parasitica colonies transfected with mutant recombinant viruses. Equal amounts (OD, 0.25) of total RNA extracted from uninfected mycelia (lane 7) and mycelia infected with CHV1-EP713 wild-type virus (lane 1) or mutant viruses Δp29 (lane 2), Δp40a (lane 3), Δp40b (lane 4), Δp69a (lane 5), and Δp69b (lane 6) were electrophoresed through a 0.7% agarose gel in the TAE buffer system (40 mM Tris-acetate-1 mM EDTA, pH 7.8) and stained with ethidium bromide. Lane M was loaded in parallel with 1-kb ladder DNA size markers (Gibco-BRL, Gaithersburg, Md.). Relative mobilities of viral dsRNA are indicated. (B) Relative accumulation of viral minus-strand RNA in fungal colonies infected with wild-type CHV1-EP713 and mutant viruses. Total RNA was isolated from mycelia infected with CHV1-EP713 (bar 1) and mutant viruses Δp29 (bar 2), Δp40a (bar 3), Δp40b (bar 4), Δp69a (bar 5), and Δp69b (bar 6) and used for strand-specific cDNA synthesis after denaturation in 90% dimethyl sulfoxide at 65°C. The resulting cDNA was subjected to semiquantitative PCR analysis in a GeneAmp 5700 sequence detection system by using cDNA of 18S rRNA generated in the same RT reaction for normalization. The sequences of primers and TaqMan probes used in the quantification are described in Methods and Materials. Viral minus-strand RNA accumulation levels are reported as percentages of the value for CHV1-EP713-infected colonies, with standard deviations based on three independent measurements indicated by the error bars.

    Techniques Used: Agarose Gel Electrophoresis, Isolation, Transfection, Mutagenesis, Recombinant, Infection, Staining, Polymerase Chain Reaction, Sequencing, Generated

    26) Product Images from "Matrix metalloproteinase 9 expression: new regulatory elements"

    Article Title: Matrix metalloproteinase 9 expression: new regulatory elements

    Journal: Journal of Ocular Biology, Diseases, and Informatics

    doi: 10.1007/s12177-010-9054-2

    Quantification of luciferase firefly mRNA by qRT-PCR using Taqman assay. The quantity of luciferase mRNA in A7 cells transfected by pGL3 control vector with inserted UTR or t340 fragments was compared with the quantity in cells transfected with intact
    Figure Legend Snippet: Quantification of luciferase firefly mRNA by qRT-PCR using Taqman assay. The quantity of luciferase mRNA in A7 cells transfected by pGL3 control vector with inserted UTR or t340 fragments was compared with the quantity in cells transfected with intact

    Techniques Used: Luciferase, Quantitative RT-PCR, TaqMan Assay, Transfection, Plasmid Preparation

    27) Product Images from "Immunodominant fragments of myelin basic protein initiate T cell-dependent pain"

    Article Title: Immunodominant fragments of myelin basic protein initiate T cell-dependent pain

    Journal: Journal of Neuroinflammation

    doi: 10.1186/1742-2094-9-119

    Acute MMP-9/2 inhibition attenuates CCI-induced allodynia and neuroinflammation. ( A ) Gelatin zymography of sciatic nerve extracts (70 μg total protein/lane) obtained at 3 h, 6 h, 1 day, 3 days, 5 days, and 7 days post-CCI. The arrows point to the MMP-9 and MMP-2 species. ( B ) Taqman qRT-PCR for MMP-9 in the sham (Sh) and CCI sciatic nerves (day 1). The mean relative mRNA ± SEM of n = 6/group normalized to GAPDH compared to naïve (N) nerve (**, P
    Figure Legend Snippet: Acute MMP-9/2 inhibition attenuates CCI-induced allodynia and neuroinflammation. ( A ) Gelatin zymography of sciatic nerve extracts (70 μg total protein/lane) obtained at 3 h, 6 h, 1 day, 3 days, 5 days, and 7 days post-CCI. The arrows point to the MMP-9 and MMP-2 species. ( B ) Taqman qRT-PCR for MMP-9 in the sham (Sh) and CCI sciatic nerves (day 1). The mean relative mRNA ± SEM of n = 6/group normalized to GAPDH compared to naïve (N) nerve (**, P

    Techniques Used: Inhibition, Zymography, Quantitative RT-PCR

    28) Product Images from "Reducing prohibitin increases histone acetylation, and promotes androgen independence in prostate tumours by increasing androgen receptor activation by adrenal androgens"

    Article Title: Reducing prohibitin increases histone acetylation, and promotes androgen independence in prostate tumours by increasing androgen receptor activation by adrenal androgens

    Journal: Oncogene

    doi: 10.1038/onc.2011.591

    Analysis of gene expression in LNCaP cell lines with altered PHB levels. (a) Taqman RT-PCR analysis of PSA transcript levels collected at time intervals (0 – 8hr) from starved LNCaP/Luc/PHB-RNAi cells treated with 10nM DHT (left hand side) or 10nM androstenedione (right hand side) with or without doxycycline. (b) Taqman RT-PCR analysis of PSA transcript levels from starved LNCaP/Luc/PHB-cDNA treated with increasing concentrations of DHT or androstenedione. (c) Taqman RT-PCR analysis of PSA transcript levels from starved LNCaP/Luc/PHB-RNAi cells treated with increasing concentrations of DHT or androstenedione (± doxycycline). (d) Luciferase activity from LNCaP/Luc/PHB-RNAi cells treated with DHT (0-100nM) or Adione (0-100nM) with or without doxycycline. Data are mean ± SD of 3 independent experiments performed in triplicate on a representative LNCaP/Luc/PHB-RNAi clone.
    Figure Legend Snippet: Analysis of gene expression in LNCaP cell lines with altered PHB levels. (a) Taqman RT-PCR analysis of PSA transcript levels collected at time intervals (0 – 8hr) from starved LNCaP/Luc/PHB-RNAi cells treated with 10nM DHT (left hand side) or 10nM androstenedione (right hand side) with or without doxycycline. (b) Taqman RT-PCR analysis of PSA transcript levels from starved LNCaP/Luc/PHB-cDNA treated with increasing concentrations of DHT or androstenedione. (c) Taqman RT-PCR analysis of PSA transcript levels from starved LNCaP/Luc/PHB-RNAi cells treated with increasing concentrations of DHT or androstenedione (± doxycycline). (d) Luciferase activity from LNCaP/Luc/PHB-RNAi cells treated with DHT (0-100nM) or Adione (0-100nM) with or without doxycycline. Data are mean ± SD of 3 independent experiments performed in triplicate on a representative LNCaP/Luc/PHB-RNAi clone.

    Techniques Used: Expressing, Reverse Transcription Polymerase Chain Reaction, Luciferase, Activity Assay

    ChIP analysis of AR and PHB on the PSA regulatory region. (a) Diagramatic representation of the PSA promoter indicating locations of ARE I, II, III and the intervening regions (negative and up/down-stream). Labelling boxes indicate amplification regions of primer pairs used for PCR. DNA immunoprecipitated with either IgG control, AR or PHB antibody was amplified by PCR and the results for each region are shown underneath, compared to their respective input DNA control. Densitometry data for each band for PHB are given underneath. (b) ChIP analysis of AR and PHB binding to the PSA promoter of LNCaP cells either grown in full serum, or hormone-starved with ±10nM DHT and for 2hr. Data represents Taqman quantification of immunoprecipitated DNA, from three replicate experiments, normalised to their input DNA controls. (c) ChIP analysis of AR binding to the PSA promoter in LNCaP/Luc/PHB-RNAi cells after treatment with DHT for 0-2hrs (± doxycycline). (d) ChIP analysis of PHB binding to the PSA promoter in LNCaP/Luc/PHB-RNAi cells after treatment with DHT for 0-2hrs (± doxycycline). Data are from a representative LNCaP/Luc/PHB-RNAi clone. ** = P
    Figure Legend Snippet: ChIP analysis of AR and PHB on the PSA regulatory region. (a) Diagramatic representation of the PSA promoter indicating locations of ARE I, II, III and the intervening regions (negative and up/down-stream). Labelling boxes indicate amplification regions of primer pairs used for PCR. DNA immunoprecipitated with either IgG control, AR or PHB antibody was amplified by PCR and the results for each region are shown underneath, compared to their respective input DNA control. Densitometry data for each band for PHB are given underneath. (b) ChIP analysis of AR and PHB binding to the PSA promoter of LNCaP cells either grown in full serum, or hormone-starved with ±10nM DHT and for 2hr. Data represents Taqman quantification of immunoprecipitated DNA, from three replicate experiments, normalised to their input DNA controls. (c) ChIP analysis of AR binding to the PSA promoter in LNCaP/Luc/PHB-RNAi cells after treatment with DHT for 0-2hrs (± doxycycline). (d) ChIP analysis of PHB binding to the PSA promoter in LNCaP/Luc/PHB-RNAi cells after treatment with DHT for 0-2hrs (± doxycycline). Data are from a representative LNCaP/Luc/PHB-RNAi clone. ** = P

    Techniques Used: Chromatin Immunoprecipitation, Amplification, Polymerase Chain Reaction, Immunoprecipitation, Binding Assay

    29) Product Images from "Transcriptomic Hallmarks of Tumor Plasticity and Stromal Interactions in Brain Metastasis"

    Article Title: Transcriptomic Hallmarks of Tumor Plasticity and Stromal Interactions in Brain Metastasis

    Journal: Cell reports

    doi: 10.1016/j.celrep.2019.03.085

    Adaptive Expression of Lineage-Specific Genes in Brain Metastatic Tumor Cells (A) Heatmap depicts normalized expression of tumor genes associated with EMT, canonical WNT signaling, and neuronal-like pathways (from gene ontology [GO] gene sets Neuron_Projection_Guidance and Regulation_of_Neuron_Differentiation). (B) A Stromal-Cancer Cell Crosstalk Network analysis identifies paracrine WNT signaling as being preferentially upregulated in tumor cells colonizing the brain. Red dots represent murine stromal ligands that are upregulated in forebrain metastasis versus in s.c. tumor samples; yellow dots represent receptors that are expressed in forebrain metastasis tumor cells; cyan dots represent pathway transcriptions factors expressed by forebrain metastasis tumor cells; and green dots represent downstream target genes upregulated in forebrain metastasis tumor cells. (C–F) Tumor mRNA expression of (C) AXIN2 , (D) NCAM1 , (E) ID2 , and (F) CDH1 was measured using species-specific TaqMan qRT-PCR and normalized to HPRT1 across all samples. H2030-BrM3 cells were grown in culture (2D; n = 3 samples) or in vivo as hindbrain metastasis (HBMet) (n = 3) or forebrain metastasis (FBMet) (n = 3). Forebrain metastases were also dissociated and re-plated in culture for three passages (FBMet→2D; n = 2). Data are presented as mean ± SEM. p values are calculated by unpaired Student’s t test. Comparisons that are not significant are not shown.
    Figure Legend Snippet: Adaptive Expression of Lineage-Specific Genes in Brain Metastatic Tumor Cells (A) Heatmap depicts normalized expression of tumor genes associated with EMT, canonical WNT signaling, and neuronal-like pathways (from gene ontology [GO] gene sets Neuron_Projection_Guidance and Regulation_of_Neuron_Differentiation). (B) A Stromal-Cancer Cell Crosstalk Network analysis identifies paracrine WNT signaling as being preferentially upregulated in tumor cells colonizing the brain. Red dots represent murine stromal ligands that are upregulated in forebrain metastasis versus in s.c. tumor samples; yellow dots represent receptors that are expressed in forebrain metastasis tumor cells; cyan dots represent pathway transcriptions factors expressed by forebrain metastasis tumor cells; and green dots represent downstream target genes upregulated in forebrain metastasis tumor cells. (C–F) Tumor mRNA expression of (C) AXIN2 , (D) NCAM1 , (E) ID2 , and (F) CDH1 was measured using species-specific TaqMan qRT-PCR and normalized to HPRT1 across all samples. H2030-BrM3 cells were grown in culture (2D; n = 3 samples) or in vivo as hindbrain metastasis (HBMet) (n = 3) or forebrain metastasis (FBMet) (n = 3). Forebrain metastases were also dissociated and re-plated in culture for three passages (FBMet→2D; n = 2). Data are presented as mean ± SEM. p values are calculated by unpaired Student’s t test. Comparisons that are not significant are not shown.

    Techniques Used: Expressing, Quantitative RT-PCR, In Vivo

    Adaptive Neuroinflammatory Response in the Brain Metastatic Stroma (A) Stromal mRNA expression of known genes expressed in astrocytes ( Gfap ) and macrophages ( C1qb ) using species-specific TaqMan qRT-PCR. Data were normalized to Hprt across all samples. Data are presented as mean ± SEM. p values are computed by unpaired Student’s t test. Forebrain metastasis (FBMet) and hindbrain metastasis (HBMet) (n = 3); hindbrain (HB) and forebrain (FB) (n = 4). Comparisons that are not significant are not shown. (B) Heatmap depicts normalized expression values of stromal genes associated with pro-inflammatory or immune-suppressive or tissue remodeling functions as determined by current literature. (C–E) Representative images of immunofluorescent (IF) staining of astrocytes (C; GFAP; red), TAMs (D; IBA1; red), neutrophils (E; LY6GG; red), and tumor cells (GFP; blue) in tumor-bearing brain (bottom) and in corresponding control regions (top). (F) Representative IF staining of microglia (TMEM119; green), TAMs (IBA1; red), and tumor (GFP; blue) in the metastatic brain. Yellow arrow indicates a TMEM119positive, IBA1-positive cell. White arrow indicates TMEM119-negative, IBA1-positive cell. Scale bars are 100 μm except where otherwise indicated.
    Figure Legend Snippet: Adaptive Neuroinflammatory Response in the Brain Metastatic Stroma (A) Stromal mRNA expression of known genes expressed in astrocytes ( Gfap ) and macrophages ( C1qb ) using species-specific TaqMan qRT-PCR. Data were normalized to Hprt across all samples. Data are presented as mean ± SEM. p values are computed by unpaired Student’s t test. Forebrain metastasis (FBMet) and hindbrain metastasis (HBMet) (n = 3); hindbrain (HB) and forebrain (FB) (n = 4). Comparisons that are not significant are not shown. (B) Heatmap depicts normalized expression values of stromal genes associated with pro-inflammatory or immune-suppressive or tissue remodeling functions as determined by current literature. (C–E) Representative images of immunofluorescent (IF) staining of astrocytes (C; GFAP; red), TAMs (D; IBA1; red), neutrophils (E; LY6GG; red), and tumor cells (GFP; blue) in tumor-bearing brain (bottom) and in corresponding control regions (top). (F) Representative IF staining of microglia (TMEM119; green), TAMs (IBA1; red), and tumor (GFP; blue) in the metastatic brain. Yellow arrow indicates a TMEM119positive, IBA1-positive cell. White arrow indicates TMEM119-negative, IBA1-positive cell. Scale bars are 100 μm except where otherwise indicated.

    Techniques Used: Expressing, Quantitative RT-PCR, Staining

    30) Product Images from "Liver-Type Fatty Acid-Binding Protein Attenuates Renal Injury Induced by Unilateral Ureteral Obstruction"

    Article Title: Liver-Type Fatty Acid-Binding Protein Attenuates Renal Injury Induced by Unilateral Ureteral Obstruction

    Journal: The American Journal of Pathology

    doi: 10.2353/ajpath.2006.060131

    Expression of MCP-3 in mice with UUO. Expression of MCP-3 mRNA transcripts was determined by TaqMan real-time PCR and was normalized to that of GAPDH mRNA transcripts in the same sample. ▪, Tg mice; □, WT mice. § P
    Figure Legend Snippet: Expression of MCP-3 in mice with UUO. Expression of MCP-3 mRNA transcripts was determined by TaqMan real-time PCR and was normalized to that of GAPDH mRNA transcripts in the same sample. ▪, Tg mice; □, WT mice. § P

    Techniques Used: Expressing, Mouse Assay, Real-time Polymerase Chain Reaction

    Expression of TGF-β in mice with UUO. Expression of TGF-β mRNA transcripts was determined by TaqMan real-time PCR and was normalized to that of GAPDH mRNA transcripts in the same sample. ▪, Tg mice; □, WT mice. # P
    Figure Legend Snippet: Expression of TGF-β in mice with UUO. Expression of TGF-β mRNA transcripts was determined by TaqMan real-time PCR and was normalized to that of GAPDH mRNA transcripts in the same sample. ▪, Tg mice; □, WT mice. # P

    Techniques Used: Expressing, Mouse Assay, Real-time Polymerase Chain Reaction

    Expression of MCP-1 in mice with UUO. a: Expression of MCP-1 mRNA transcripts was determined by TaqMan real-time PCR and was normalized to that of GAPDH mRNA transcripts in the same sample. b: The expression of MCP-1 protein was determined by ELISA and was corrected for the total amount of protein. Values are the mean ± SE. ▪, Tg mice; □, WT mice. § P
    Figure Legend Snippet: Expression of MCP-1 in mice with UUO. a: Expression of MCP-1 mRNA transcripts was determined by TaqMan real-time PCR and was normalized to that of GAPDH mRNA transcripts in the same sample. b: The expression of MCP-1 protein was determined by ELISA and was corrected for the total amount of protein. Values are the mean ± SE. ▪, Tg mice; □, WT mice. § P

    Techniques Used: Expressing, Mouse Assay, Real-time Polymerase Chain Reaction, Enzyme-linked Immunosorbent Assay

    UUO-induced expression of hL-FABP in Tg mice. a: The expression of hL-FABP transcripts was determined by TaqMan real-time PCR and was normalized to GAPDH. b: The expression of hL-FABP protein was determined by ELISA and was corrected for the total amount of protein. Values are mean ± SE. * P
    Figure Legend Snippet: UUO-induced expression of hL-FABP in Tg mice. a: The expression of hL-FABP transcripts was determined by TaqMan real-time PCR and was normalized to GAPDH. b: The expression of hL-FABP protein was determined by ELISA and was corrected for the total amount of protein. Values are mean ± SE. * P

    Techniques Used: Expressing, Mouse Assay, Real-time Polymerase Chain Reaction, Enzyme-linked Immunosorbent Assay

    Expression of Gpx1 in mice with UUO. The expression of Gpx1 mRNΑ transcripts was determined by TaqMan real-time PCR and was normalized to that of GAPDH in the same sample. ▪, Tg mice; □, WT mice. # P
    Figure Legend Snippet: Expression of Gpx1 in mice with UUO. The expression of Gpx1 mRNΑ transcripts was determined by TaqMan real-time PCR and was normalized to that of GAPDH in the same sample. ▪, Tg mice; □, WT mice. # P

    Techniques Used: Expressing, Mouse Assay, Real-time Polymerase Chain Reaction

    Expression of HO-1 in mice with UUO. The expression of HO-1 mRNΑ transcripts was determined by TaqMan real-time PCR and was normalized to that of GAPDH in the same sample. ▪, Tg mice; □, WT mice. # P
    Figure Legend Snippet: Expression of HO-1 in mice with UUO. The expression of HO-1 mRNΑ transcripts was determined by TaqMan real-time PCR and was normalized to that of GAPDH in the same sample. ▪, Tg mice; □, WT mice. # P

    Techniques Used: Expressing, Mouse Assay, Real-time Polymerase Chain Reaction

    31) Product Images from "Hepatoprotectant Ursodeoxycholyl Lysophosphatidylethanolamide Increasing Phosphatidylcholine Levels as a Potential Therapy of Acute Liver Injury"

    Article Title: Hepatoprotectant Ursodeoxycholyl Lysophosphatidylethanolamide Increasing Phosphatidylcholine Levels as a Potential Therapy of Acute Liver Injury

    Journal: Frontiers in Physiology

    doi: 10.3389/fphys.2012.00024

    Ursodeoxycholyl lysophosphatidylethanolamide upregulated CDS1 gene concomitant with inhibition of apoptosis induced by palmitate . (A) Treatment of mouse hepatocytes with 60 μM UDCA-LPE for 20 h increased expression of CDS1 but failed to increase other PC synthesis genes including choline kinase, CDS2, CEPT2, CEPT, CCTalpha, and PEMT. Quantitative RT-PCR was performed by TaqMan ® RT-PCR with relative expression (Δ Rn ) of the target gene versus GAPDH mRNA. Data were representative data obtained from two different experiments. Data were mean ± SD, N = 4; * p
    Figure Legend Snippet: Ursodeoxycholyl lysophosphatidylethanolamide upregulated CDS1 gene concomitant with inhibition of apoptosis induced by palmitate . (A) Treatment of mouse hepatocytes with 60 μM UDCA-LPE for 20 h increased expression of CDS1 but failed to increase other PC synthesis genes including choline kinase, CDS2, CEPT2, CEPT, CCTalpha, and PEMT. Quantitative RT-PCR was performed by TaqMan ® RT-PCR with relative expression (Δ Rn ) of the target gene versus GAPDH mRNA. Data were representative data obtained from two different experiments. Data were mean ± SD, N = 4; * p

    Techniques Used: Inhibition, Expressing, Quantitative RT-PCR, Reverse Transcription Polymerase Chain Reaction

    32) Product Images from "Expression and functional analysis of citrus carotene hydroxylases: unravelling the xanthophyll biosynthesis in citrus fruits"

    Article Title: Expression and functional analysis of citrus carotene hydroxylases: unravelling the xanthophyll biosynthesis in citrus fruits

    Journal: BMC Plant Biology

    doi: 10.1186/s12870-016-0840-2

    Changes in the expression of carotene hydroxylase genes in the flavedo ( a ) and juice sacs ( b ) during the ripening process. The results shown are the mean ± SE for triplicate samples. The mRNA levels were analyzed by TaqMan real-time quantitative RT-PCR. Real-time RT-PCR amplification of 18S rRNA was used to normalize the expression of the genes under identical conditions. A, August; S, September; O, October; N, November; D, December
    Figure Legend Snippet: Changes in the expression of carotene hydroxylase genes in the flavedo ( a ) and juice sacs ( b ) during the ripening process. The results shown are the mean ± SE for triplicate samples. The mRNA levels were analyzed by TaqMan real-time quantitative RT-PCR. Real-time RT-PCR amplification of 18S rRNA was used to normalize the expression of the genes under identical conditions. A, August; S, September; O, October; N, November; D, December

    Techniques Used: Expressing, Quantitative RT-PCR, Amplification

    33) Product Images from "PR-Independent Neurosteroid Regulation of α2-GABA-A Receptors in the Hippocampus Subfields"

    Article Title: PR-Independent Neurosteroid Regulation of α2-GABA-A Receptors in the Hippocampus Subfields

    Journal: Brain research

    doi: 10.1016/j.brainres.2017.01.030

    Changes in GABA-A receptor α2-subunit mRNA expression in the hippocampus subfields CA1, CA3, and dentate gyrus (DG) during various phases of the estrous cycle Total RNA was extracted from the microdisected hippocampus tissue and cDNA was prepared for TaqMan PCR analysis. The TaqMan PCR data was normalized in every assay using GAPDH and expressed as percent over the control. The data represents the mean ±SEM (n=8 mice per group). *p
    Figure Legend Snippet: Changes in GABA-A receptor α2-subunit mRNA expression in the hippocampus subfields CA1, CA3, and dentate gyrus (DG) during various phases of the estrous cycle Total RNA was extracted from the microdisected hippocampus tissue and cDNA was prepared for TaqMan PCR analysis. The TaqMan PCR data was normalized in every assay using GAPDH and expressed as percent over the control. The data represents the mean ±SEM (n=8 mice per group). *p

    Techniques Used: Expressing, Polymerase Chain Reaction, Mouse Assay

    34) Product Images from "The novel histone deacetylase inhibitor, LBH589, induces expression of DNA damage response genes and apoptosis in Ph− acute lymphoblastic leukemia cells"

    Article Title: The novel histone deacetylase inhibitor, LBH589, induces expression of DNA damage response genes and apoptosis in Ph− acute lymphoblastic leukemia cells

    Journal:

    doi: 10.1182/blood-2007-10-117762

    LBH589 induces expression of GADD45G mRNA and enhances acetylation of histones at the GADD45G promoter in MOLT-4 and Reh cells. (A) Following treatment with 50 nM LBH589 for 24 hours, TaqMan real-time PCR was performed on MOLT-4 and Reh cells. The mRNA
    Figure Legend Snippet: LBH589 induces expression of GADD45G mRNA and enhances acetylation of histones at the GADD45G promoter in MOLT-4 and Reh cells. (A) Following treatment with 50 nM LBH589 for 24 hours, TaqMan real-time PCR was performed on MOLT-4 and Reh cells. The mRNA

    Techniques Used: Expressing, Real-time Polymerase Chain Reaction

    LBH589 induces expression of GADD45G mRNA in cultured primary Ph − ALL cells. Following treatment with 50 nM LBH589 for 24 hours, TaqMan real-time PCR was performed on the cDNA from 6 patient samples. The mRNA levels were normalized to levels of
    Figure Legend Snippet: LBH589 induces expression of GADD45G mRNA in cultured primary Ph − ALL cells. Following treatment with 50 nM LBH589 for 24 hours, TaqMan real-time PCR was performed on the cDNA from 6 patient samples. The mRNA levels were normalized to levels of

    Techniques Used: Expressing, Cell Culture, Real-time Polymerase Chain Reaction

    35) Product Images from "Elevated MiR-222-3p Promotes Proliferation and Invasion of Endometrial Carcinoma via Targeting ER?"

    Article Title: Elevated MiR-222-3p Promotes Proliferation and Invasion of Endometrial Carcinoma via Targeting ER?

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0087563

    The expression of miR-222-3p correlated with ERα and clinicopathological parameters in endometrial carcinoma. (A) MiR-222-3p expression level was much higher in ERα-negative ECs than in ERα-positive samples. (B, C and D) Expression of miR-222-3p across different grades, stages and nodal metastasis status. MiR-222-3p expression level was positively correlated with poor clinicopathological parameters. (E and F) MiR-222-3p and ERα expression were inversely related in ECs and normal endometrium tissues. These tissues were analyzed for miR-222-3p expression by TaqMan based qRT-PCR, followed by immunohistochemistry for ERα as described in “ Materials and Methods ”. (G) Expression of miR-222-3p in cells with different ERα status. MCF-7 and RL95-2 cells were ERα-positive, while KLE and AN3CA cells were ERα-negative. Conversely, miR-222-3p expression was negative-related with ERα status. Bars are standard deviation (SD). The experiments were repeated three times. ** P
    Figure Legend Snippet: The expression of miR-222-3p correlated with ERα and clinicopathological parameters in endometrial carcinoma. (A) MiR-222-3p expression level was much higher in ERα-negative ECs than in ERα-positive samples. (B, C and D) Expression of miR-222-3p across different grades, stages and nodal metastasis status. MiR-222-3p expression level was positively correlated with poor clinicopathological parameters. (E and F) MiR-222-3p and ERα expression were inversely related in ECs and normal endometrium tissues. These tissues were analyzed for miR-222-3p expression by TaqMan based qRT-PCR, followed by immunohistochemistry for ERα as described in “ Materials and Methods ”. (G) Expression of miR-222-3p in cells with different ERα status. MCF-7 and RL95-2 cells were ERα-positive, while KLE and AN3CA cells were ERα-negative. Conversely, miR-222-3p expression was negative-related with ERα status. Bars are standard deviation (SD). The experiments were repeated three times. ** P

    Techniques Used: Expressing, Quantitative RT-PCR, Immunohistochemistry, Standard Deviation

    36) Product Images from "Mutation Detection by Real-Time PCR: A Simple, Robust and Highly Selective Method"

    Article Title: Mutation Detection by Real-Time PCR: A Simple, Robust and Highly Selective Method

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0004584

    Sensitivity and selectivity of the Mut1.2 assay. A. Detection of cell line RNA containing Kras G216T mutant diluted into wild type cell line RNA using the Kras Mut1.2 assay. ΔR n is the difference between the normalized fluorescence of the TaqMan reporter probe at each PCR cycle and the background fluorescence measured during the first 15 PCR cycles. Each curve represents the time course of PCR assays (average of triplicate measurements) at each dilution. The horizontal line at ΔR n = 0.2 represents the threshold for determination of C T for the individual amplification curves. B. Serial-dilutions of RNA extracted from wild type COLO320 (filled squares) and mutant SW480 (filled circles) cell lines submitted to the Kras Mut1.2 assay. Error bars represent 2 times the standard deviation of triplicate determinations.
    Figure Legend Snippet: Sensitivity and selectivity of the Mut1.2 assay. A. Detection of cell line RNA containing Kras G216T mutant diluted into wild type cell line RNA using the Kras Mut1.2 assay. ΔR n is the difference between the normalized fluorescence of the TaqMan reporter probe at each PCR cycle and the background fluorescence measured during the first 15 PCR cycles. Each curve represents the time course of PCR assays (average of triplicate measurements) at each dilution. The horizontal line at ΔR n = 0.2 represents the threshold for determination of C T for the individual amplification curves. B. Serial-dilutions of RNA extracted from wild type COLO320 (filled squares) and mutant SW480 (filled circles) cell lines submitted to the Kras Mut1.2 assay. Error bars represent 2 times the standard deviation of triplicate determinations.

    Techniques Used: Mutagenesis, Fluorescence, Polymerase Chain Reaction, Amplification, Standard Deviation

    37) Product Images from "Spinal activity of interleukin 6 mediates myelin basic protein-induced allodynia"

    Article Title: Spinal activity of interleukin 6 mediates myelin basic protein-induced allodynia

    Journal: Brain, behavior, and immunity

    doi: 10.1016/j.bbi.2016.03.003

    Unilateral increase in spinal IL-6 expression after IS MBP A, A schematic diagram: after IS injection of MBP84-104 or scrambled (s)MBP84-104 peptides (50 μg in 5 μl, each) into naïve sciatic nerve, ipsilateral or contralateral nerve, DRG and spinal cord (dorsal quarter) samples were analyzed. B , IL-6 Taqman qRT-PCR at day 7 after A. or CCI (positive control). The mean relative mRNA ± SEM of n=3–5/group normalized to GAPDH and calibrated to naïve tissues; y, log scale (*, p≤0.05, n.s., not significant (p > 0.05), compared with the scrambled peptide; # , p≤0.05 compared with naïve; by 2-way ANOVA with Tukey-Kramer posthoc).
    Figure Legend Snippet: Unilateral increase in spinal IL-6 expression after IS MBP A, A schematic diagram: after IS injection of MBP84-104 or scrambled (s)MBP84-104 peptides (50 μg in 5 μl, each) into naïve sciatic nerve, ipsilateral or contralateral nerve, DRG and spinal cord (dorsal quarter) samples were analyzed. B , IL-6 Taqman qRT-PCR at day 7 after A. or CCI (positive control). The mean relative mRNA ± SEM of n=3–5/group normalized to GAPDH and calibrated to naïve tissues; y, log scale (*, p≤0.05, n.s., not significant (p > 0.05), compared with the scrambled peptide; # , p≤0.05 compared with naïve; by 2-way ANOVA with Tukey-Kramer posthoc).

    Techniques Used: Expressing, Injection, Quantitative RT-PCR, Positive Control

    IL-6 inhibitor, intrathecally delivered, reduces MBP-induced allodynia A , von Frey testing after IS injection of MBP84-104 (n=15) or scrambled (s)MBP84-104 (n=3), 50 μg in 5 μl each, into naïve sciatic nerve, or in naïve rats (n=5). Goat IL-6 function-blocking antibody (IL6i, n=8) or normal goat IgG (n=7), 5 ng/μl each, was delivered IT at day 7 post-IS injection. The withdrawal thresholds in the ipsilateral hind paw showed gradual reduction of mechanical allodynia. B, An area-under-the-curve (AUC) analysis of A. from days 7–10 post-injection. The mean withdrawal thresholds (gram force, g) ± SEM (**, p≤0.01; ***, p≤0.001; ****, p≤0.0001, by 2-way ANOVA with Bonferoni post-hoc, comparing to day 7 baseline and excluding sMBP84-104 +IL6i group due to small group size). C, ATF3 and Cacna2d1 Taqman qRT-PCR in DRG after completion of A–B, at day 10 post-injection. The mean relative mRNA ± SEM of n=3/group normalized to GAPDH calibrated to naïve DRG (*, p≤0.05; **, p≤0.01, by 2-way ANOVA with Tukey-Kramer posthoc). D–E, IL-6R immunofluorescence alone (D–E, green) and dual-stained with GFAP (E, satellite cell marker, red, top panel) or large ATF3+ neurons (E, red, bottom panel) in DRG at day 7 after IS MBP84-104. DAPI (blue). Arrows: co-distribution. Representative of n=4. Scale bars: 15 μm.
    Figure Legend Snippet: IL-6 inhibitor, intrathecally delivered, reduces MBP-induced allodynia A , von Frey testing after IS injection of MBP84-104 (n=15) or scrambled (s)MBP84-104 (n=3), 50 μg in 5 μl each, into naïve sciatic nerve, or in naïve rats (n=5). Goat IL-6 function-blocking antibody (IL6i, n=8) or normal goat IgG (n=7), 5 ng/μl each, was delivered IT at day 7 post-IS injection. The withdrawal thresholds in the ipsilateral hind paw showed gradual reduction of mechanical allodynia. B, An area-under-the-curve (AUC) analysis of A. from days 7–10 post-injection. The mean withdrawal thresholds (gram force, g) ± SEM (**, p≤0.01; ***, p≤0.001; ****, p≤0.0001, by 2-way ANOVA with Bonferoni post-hoc, comparing to day 7 baseline and excluding sMBP84-104 +IL6i group due to small group size). C, ATF3 and Cacna2d1 Taqman qRT-PCR in DRG after completion of A–B, at day 10 post-injection. The mean relative mRNA ± SEM of n=3/group normalized to GAPDH calibrated to naïve DRG (*, p≤0.05; **, p≤0.01, by 2-way ANOVA with Tukey-Kramer posthoc). D–E, IL-6R immunofluorescence alone (D–E, green) and dual-stained with GFAP (E, satellite cell marker, red, top panel) or large ATF3+ neurons (E, red, bottom panel) in DRG at day 7 after IS MBP84-104. DAPI (blue). Arrows: co-distribution. Representative of n=4. Scale bars: 15 μm.

    Techniques Used: Injection, Blocking Assay, Quantitative RT-PCR, Immunofluorescence, Staining, Marker

    38) Product Images from "Real-Time PCR Detection of Phaeomoniella chlamydospora and Phaeoacremonium aleophilum"

    Article Title: Real-Time PCR Detection of Phaeomoniella chlamydospora and Phaeoacremonium aleophilum

    Journal: Applied and Environmental Microbiology

    doi: 10.1128/AEM.07360-11

    (ii) TaqMan PCR.
    Figure Legend Snippet: (ii) TaqMan PCR.

    Techniques Used: Polymerase Chain Reaction

    (ii) TaqMan PCR.
    Figure Legend Snippet: (ii) TaqMan PCR.

    Techniques Used: Polymerase Chain Reaction

    (ii) TaqMan PCR.
    Figure Legend Snippet: (ii) TaqMan PCR.

    Techniques Used: Polymerase Chain Reaction

    (ii) TaqMan PCR.
    Figure Legend Snippet: (ii) TaqMan PCR.

    Techniques Used: Polymerase Chain Reaction

    39) Product Images from "Autocrine/paracrine cytokine stimulation of leukemic cell proliferation in smoldering and chronic adult T-cell leukemia"

    Article Title: Autocrine/paracrine cytokine stimulation of leukemic cell proliferation in smoldering and chronic adult T-cell leukemia

    Journal: Blood

    doi: 10.1182/blood-2010-04-277418

    IL-2 signaling was required for optimal IL-9 expression in ex vivo cultures of PBMCs from patients with smoldering/chronic ATL . (A) IL-2, IL-9, and Tax mRNA levels were determined every day in ex vivo cultures by TaqMan real-time RT-PCR. The copy numbers
    Figure Legend Snippet: IL-2 signaling was required for optimal IL-9 expression in ex vivo cultures of PBMCs from patients with smoldering/chronic ATL . (A) IL-2, IL-9, and Tax mRNA levels were determined every day in ex vivo cultures by TaqMan real-time RT-PCR. The copy numbers

    Techniques Used: Expressing, Ex Vivo, Quantitative RT-PCR

    40) Product Images from "Analysis of neonatal brain lacking ATRX or MeCP2 reveals changes in nucleosome density, CTCF binding and chromatin looping"

    Article Title: Analysis of neonatal brain lacking ATRX or MeCP2 reveals changes in nucleosome density, CTCF binding and chromatin looping

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gku564

    ATRX and MeCP2 regulate nucleosome positioning and long-range chromatin interactions mediated by the Gtl2 DMR. ( a ) 4C-sequencing analysis using the Gtl2 DMR as bait was performed in wild-type neonatal forebrains. Venn diagrams show the number of common sequences between 4C-seq biological replicates. Interactions of the Gtl2 DMR in trans are represented on the left and interactions in cis are represented on the right. ( b ) Analysis of genomic distribution of Gtl2 DMR-interacting fragments on each chromosome reveals that the majority of reproducible interactions occur within chromosome 12 while trans interactions are distributed across the genome, with a noted enrichment on the sex chromosomes. ( c ) Schematic representation of the Gtl2/Dlk1 genomic region, the position of EcoRI sites (black vertical lines) and the primers used for 3C analysis (black arrows). Gray boxes represent the position of genes and black boxes demarcate regulatory elements. Numbers indicate the relative nucleotide position from the start of Gtl2 . The Gtl2 DMR bait sequence is highlighted in yellow. ( d ) For 3C analysis, DNA was digested with EcoRI, ligated and quantified by real-time PCR with a forward primer (red arrow) and Taqman probe to the Gtl2 DMR (asterisk), and reverse primers (black arrows). Analysis was performed in control and ATRX-null or control and MeCP2-null neonatal forebrains ( n = 3 littermate matched pairs each). A significant reduction in interaction frequency is observed at specific sites including the Dlk1 gene and many intergenic regions. Graphed data represents the mean fold change, and error bars depict SEM. A two-tailed t -test was used to assess significance. * P
    Figure Legend Snippet: ATRX and MeCP2 regulate nucleosome positioning and long-range chromatin interactions mediated by the Gtl2 DMR. ( a ) 4C-sequencing analysis using the Gtl2 DMR as bait was performed in wild-type neonatal forebrains. Venn diagrams show the number of common sequences between 4C-seq biological replicates. Interactions of the Gtl2 DMR in trans are represented on the left and interactions in cis are represented on the right. ( b ) Analysis of genomic distribution of Gtl2 DMR-interacting fragments on each chromosome reveals that the majority of reproducible interactions occur within chromosome 12 while trans interactions are distributed across the genome, with a noted enrichment on the sex chromosomes. ( c ) Schematic representation of the Gtl2/Dlk1 genomic region, the position of EcoRI sites (black vertical lines) and the primers used for 3C analysis (black arrows). Gray boxes represent the position of genes and black boxes demarcate regulatory elements. Numbers indicate the relative nucleotide position from the start of Gtl2 . The Gtl2 DMR bait sequence is highlighted in yellow. ( d ) For 3C analysis, DNA was digested with EcoRI, ligated and quantified by real-time PCR with a forward primer (red arrow) and Taqman probe to the Gtl2 DMR (asterisk), and reverse primers (black arrows). Analysis was performed in control and ATRX-null or control and MeCP2-null neonatal forebrains ( n = 3 littermate matched pairs each). A significant reduction in interaction frequency is observed at specific sites including the Dlk1 gene and many intergenic regions. Graphed data represents the mean fold change, and error bars depict SEM. A two-tailed t -test was used to assess significance. * P

    Techniques Used: Sequencing, Real-time Polymerase Chain Reaction, Two Tailed Test

    3C analysis of control and ATRX-deficient neonatal forebrain shows that ATRX is required for long-range chromosomal interactions mediated by the H19 ICR. ( a ) Analysis of ATRX ChIP-sequencing data in mouse embryonic stem cells ( 15 ) shows ATRX occupancy at several imprinted domains (left panels, UCSC views). ATRX enrichment at these sites in neonatal mouse forebrain was confirmed by ChIP, as shown in the graphs on the left ( n = 3, error bars represent SEM, p = peak, adj = adjacent). ( b ) Schematic representation of the H19/Igf2 genomic region, the position of EcoRI sites (gray vertical lines) and the primers used for 3C analysis (black arrows). Gray boxes represent the position of genes and black boxes demarcate regulatory elements. Numbers indicate the relative nucleotide position from the start of the H19 ICR. The H19 ICR bait sequence is highlighted in yellow. 3C analysis was performed with the H19 ICR bait and primers across the H19/Igf2 domain in control and ATRX-null forebrains ( n = 5 littermate pairs) and was quantified by PCR with a forward primer (red arrow), Taqman probe to the H19 ICR (asterisk), and reverse primers. Graphed data represents the mean fold change of interaction frequencies, and error bars depict SEM. A two-tailed t -test was used to assess significance. * P
    Figure Legend Snippet: 3C analysis of control and ATRX-deficient neonatal forebrain shows that ATRX is required for long-range chromosomal interactions mediated by the H19 ICR. ( a ) Analysis of ATRX ChIP-sequencing data in mouse embryonic stem cells ( 15 ) shows ATRX occupancy at several imprinted domains (left panels, UCSC views). ATRX enrichment at these sites in neonatal mouse forebrain was confirmed by ChIP, as shown in the graphs on the left ( n = 3, error bars represent SEM, p = peak, adj = adjacent). ( b ) Schematic representation of the H19/Igf2 genomic region, the position of EcoRI sites (gray vertical lines) and the primers used for 3C analysis (black arrows). Gray boxes represent the position of genes and black boxes demarcate regulatory elements. Numbers indicate the relative nucleotide position from the start of the H19 ICR. The H19 ICR bait sequence is highlighted in yellow. 3C analysis was performed with the H19 ICR bait and primers across the H19/Igf2 domain in control and ATRX-null forebrains ( n = 5 littermate pairs) and was quantified by PCR with a forward primer (red arrow), Taqman probe to the H19 ICR (asterisk), and reverse primers. Graphed data represents the mean fold change of interaction frequencies, and error bars depict SEM. A two-tailed t -test was used to assess significance. * P

    Techniques Used: Chromatin Immunoprecipitation, Sequencing, Polymerase Chain Reaction, Two Tailed Test

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    Derivative Assay:

    Article Title: Carrot yellow leaf virus Is Associated with Carrot Internal Necrosis
    Article Snippet: .. Real-time PCR Real-time (TaqMan) primers and probes were designed using Primer Express 2 with sequences from GenBank and derived from the sequencing in this study when available (Applied Biosystems). .. Real-time RT-PCR was performed on previously extracted RNA in 96 well plates on an ABI 7900 instrument (Applied Biosystems).

    Software:

    Article Title: Expression of CtBP family protein isoforms in breast cancer and their role in chemoresistance
    Article Snippet: .. TaqMan quantitative PCR for CTBP1 and CTBP2 was performed using commercial primer/probe sets (Applied Biosystems; Assays on Demand Hs00972288_g1 and Hs00949547_g1 respectively) using the ABI PRISM 7900HT instrument and software (PerkinElmer Life Sciences). ..

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    Thermo Fisher universal pcr master mix
    The microRNA (miR)-96/182/183 cluster is upregulated in the livers of colesevelam-treated Zucker diabetic fatty (ZDF) rats. A : volcano plot depicting significantly altered miRNAs between colesevelam (Col) and vehicle-treated ZDF rat livers ( left ) and expression (reads per million total reads) of the miR-96/182/183 cluster ( left ); n = 6. B–D : liver expression of the miR-96/182/183 cluster by real-time <t>PCR;</t> n = 9–12. E : liver gene (mRNA) expression changes of Srebf2 and its target genes Hmgcr , Ldlr , and Sqle ; n = 8–12. For sequencing data, unpaired t -tests were used. For comparisons between 2 groups, Mann-Whitney nonparametric tests were used; n.d., not detectable.
    Universal Pcr Master Mix, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 85/100, based on 9357 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Thermo Fisher taqman universal master mix ii
    Dysregulation of <t>miR-125b</t> and miR-22 expression in RNA extracted from prostate tissue samples by LCM. (A) Frozen prostate samples were dissected via LCM into benign glandular epithelial versus tumor. Total RNA was extracted using the PicoPure RNA extraction method, as described in Materials and Methods. qRT-PCR was performed with specific primers against miR-125b and miR-22 using the <t>TaqMan</t> ® Universal Master Mix II. C T values were normalized to RNU48 and reported as fold differences compared to benign tissue using the ΔΔCT method of Livak et al. [ 23 ]. Results are the average from frozen tissue samples (n = 4) repeated in 3 technical replicates. (B) From 10 successive slides of a single FFPE prostate sample, miR-125b was quantitated by qRT-PCR as described in panel A for RNA extracted from stroma, benign glandular tissue, BPH, PIN and tumor of stage G4.
    Taqman Universal Master Mix Ii, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 611 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/taqman universal master mix ii/product/Thermo Fisher
    Average 99 stars, based on 611 article reviews
    Price from $9.99 to $1999.99
    taqman universal master mix ii - by Bioz Stars, 2021-01
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    Image Search Results


    The microRNA (miR)-96/182/183 cluster is upregulated in the livers of colesevelam-treated Zucker diabetic fatty (ZDF) rats. A : volcano plot depicting significantly altered miRNAs between colesevelam (Col) and vehicle-treated ZDF rat livers ( left ) and expression (reads per million total reads) of the miR-96/182/183 cluster ( left ); n = 6. B–D : liver expression of the miR-96/182/183 cluster by real-time PCR; n = 9–12. E : liver gene (mRNA) expression changes of Srebf2 and its target genes Hmgcr , Ldlr , and Sqle ; n = 8–12. For sequencing data, unpaired t -tests were used. For comparisons between 2 groups, Mann-Whitney nonparametric tests were used; n.d., not detectable.

    Journal: American Journal of Physiology - Gastrointestinal and Liver Physiology

    Article Title: Liver and Biliary Tract Physiology/Pathophysiology: Intestinal bile acid sequestration improves glucose control by stimulating hepatic miR-182-5p in type 2 diabetes

    doi: 10.1152/ajpgi.00238.2018

    Figure Lengend Snippet: The microRNA (miR)-96/182/183 cluster is upregulated in the livers of colesevelam-treated Zucker diabetic fatty (ZDF) rats. A : volcano plot depicting significantly altered miRNAs between colesevelam (Col) and vehicle-treated ZDF rat livers ( left ) and expression (reads per million total reads) of the miR-96/182/183 cluster ( left ); n = 6. B–D : liver expression of the miR-96/182/183 cluster by real-time PCR; n = 9–12. E : liver gene (mRNA) expression changes of Srebf2 and its target genes Hmgcr , Ldlr , and Sqle ; n = 8–12. For sequencing data, unpaired t -tests were used. For comparisons between 2 groups, Mann-Whitney nonparametric tests were used; n.d., not detectable.

    Article Snippet: Real-time PCR was completed with Universal PCR Master Mix and TaqMan mRNA and miRNA assays (ThermoFisher).

    Techniques: Expressing, Real-time Polymerase Chain Reaction, Sequencing, MANN-WHITNEY

    Mediator complex subunit 1 (Med1) is regulated by microRNA (miR)-96/182/183 in mice. A : expression of Med1 by real-time PCR in mouse primary hepatocytes transfected with 50 nM of Med1 or scramble siRNA; n = 3 B : Western blot of Med1 and β-actin (loading control) from protein samples of primary hepatocytes transfected with Med1 or scramble siRNA. Ratio of Med1/β-actin densitometry is indicated between the blots and graphed on the right ; n = 3. A.U., arbitrary units. C : hepatic Med1 mRNA levels in db/db mice treated with vehicle or 2% colesevelam (Col)-supplemented diet and PBS or locked-nucleic acid (LNA)-182-5p; real-time PCR; n = 8–9. D : hepatic Med1 and β-actin (loading control) protein levels from 3 representative liver protein samples for Chow + PBS, Col + PBS, and Col + LNA-182. Western blotting. Ratio of Med1/β-actin densitometry is indicated between the blots. E : densitometry quantification of Med1 protein levels normalized to β-actin; n = 8–9. F : expression of miR-96-5p, miR-182-5p, and miR-183-5p in mouse primary hepatocytes transfected with 50 nM miR-96-5p, miR-182-5p, miR-183-5p mimics individually or in combination; real-time PCR; n = 3. G : Med1 mRNA levels in mouse primary hepatocytes transfected with 50 nM miR-96-5p, miR-182-5p, and miR-183-5p mimics individually or in combination; real-time PCR; n = 3. H : protein levels of Med1 and β-actin (loading control) from protein samples of primary hepatocytes transfected with mock or 50 nM miR-96-5p, miR-182-5p, and miR-183-5p mimics individually or in combination. Ratio of Med1/β-actin densitometry is indicated between the blots and graphed on the right ; n = 3. For comparisons between 2 groups, Students’ t- tests were used, and for more than 2 groups, Kruskal-Wallis one-way ANOVA with Dunn’s posttest was used (α = 0.05) or one-way ANOVA with Bonferonni’s posttest for comparison to mock group only was used (α = 0.05).

    Journal: American Journal of Physiology - Gastrointestinal and Liver Physiology

    Article Title: Liver and Biliary Tract Physiology/Pathophysiology: Intestinal bile acid sequestration improves glucose control by stimulating hepatic miR-182-5p in type 2 diabetes

    doi: 10.1152/ajpgi.00238.2018

    Figure Lengend Snippet: Mediator complex subunit 1 (Med1) is regulated by microRNA (miR)-96/182/183 in mice. A : expression of Med1 by real-time PCR in mouse primary hepatocytes transfected with 50 nM of Med1 or scramble siRNA; n = 3 B : Western blot of Med1 and β-actin (loading control) from protein samples of primary hepatocytes transfected with Med1 or scramble siRNA. Ratio of Med1/β-actin densitometry is indicated between the blots and graphed on the right ; n = 3. A.U., arbitrary units. C : hepatic Med1 mRNA levels in db/db mice treated with vehicle or 2% colesevelam (Col)-supplemented diet and PBS or locked-nucleic acid (LNA)-182-5p; real-time PCR; n = 8–9. D : hepatic Med1 and β-actin (loading control) protein levels from 3 representative liver protein samples for Chow + PBS, Col + PBS, and Col + LNA-182. Western blotting. Ratio of Med1/β-actin densitometry is indicated between the blots. E : densitometry quantification of Med1 protein levels normalized to β-actin; n = 8–9. F : expression of miR-96-5p, miR-182-5p, and miR-183-5p in mouse primary hepatocytes transfected with 50 nM miR-96-5p, miR-182-5p, miR-183-5p mimics individually or in combination; real-time PCR; n = 3. G : Med1 mRNA levels in mouse primary hepatocytes transfected with 50 nM miR-96-5p, miR-182-5p, and miR-183-5p mimics individually or in combination; real-time PCR; n = 3. H : protein levels of Med1 and β-actin (loading control) from protein samples of primary hepatocytes transfected with mock or 50 nM miR-96-5p, miR-182-5p, and miR-183-5p mimics individually or in combination. Ratio of Med1/β-actin densitometry is indicated between the blots and graphed on the right ; n = 3. For comparisons between 2 groups, Students’ t- tests were used, and for more than 2 groups, Kruskal-Wallis one-way ANOVA with Dunn’s posttest was used (α = 0.05) or one-way ANOVA with Bonferonni’s posttest for comparison to mock group only was used (α = 0.05).

    Article Snippet: Real-time PCR was completed with Universal PCR Master Mix and TaqMan mRNA and miRNA assays (ThermoFisher).

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

    Mediator complex subunit 1 (MED1) is a direct target of microRNA (miR)-182-5p, miR-183-5p, and miR-96-5p in humans. A : schematic of human MED1 mRNA and the 3 putative miR-182/183/96 target sites in the 3′-untranslated region (3′-UTR). B : predicted MED1 3′-UTR target sites. Bases highlighted in dark gray represent mutations for gene reporter (luciferase) assays. C : normalized luciferase activity in HEK293 cells after dual transfection of miR-96/182/183 mimics and gene (luciferase) reporters harboring putative target sites for miR-96-5p, miR-182-5p, and/or miR-183-5p; n = 4. D : miR-96-5p, miR-182-5p, and miR-183-5p levels in Huh7 cells transfected with 50 nM miR-96-5p, miR-182-5p, and miR-183-5p mimics individually or in combination; real-time PCR; n = 6. E : MED1 mRNA levels in Huh7 cells transfected with 50 nM miR-96-5p, miR-182-5p, and miR-183-5p mimics individually or in combination; real-time PCR; n = 6. F : miR-96-5p, miR-182-5p, and miR-183-5p levels in Huh7 cells transfected with mock or 50 nM locked-nucleic acids (LNAs) against miR-182-5p and/or miR-183-5p; real-time PCR; n = 6. G : MED1 mRNA levels in Huh7 cells transfected mock or 50 nM LNAs against miR-182-5p and/or miR-183-5p; real-time PCR; n = 6. H : protein levels of Med1 and β-actin (loading control) from protein lysates of Huh7 cells transfected with mock or 50 nM miR-96, miR-182, and miR-183 LNAs. Ratio of Med1/β-actin densitometry is indicated between the blots and graphed on the right ; n = 6. A.U. arbitrary units. For comparisons between more than 2 groups to mock only, one-way ANOVA with Bonferonni’s posttest was used, α = 0.05. For comparisons between 2 groups, Mann-Whitney nonparametric tests were used.

    Journal: American Journal of Physiology - Gastrointestinal and Liver Physiology

    Article Title: Liver and Biliary Tract Physiology/Pathophysiology: Intestinal bile acid sequestration improves glucose control by stimulating hepatic miR-182-5p in type 2 diabetes

    doi: 10.1152/ajpgi.00238.2018

    Figure Lengend Snippet: Mediator complex subunit 1 (MED1) is a direct target of microRNA (miR)-182-5p, miR-183-5p, and miR-96-5p in humans. A : schematic of human MED1 mRNA and the 3 putative miR-182/183/96 target sites in the 3′-untranslated region (3′-UTR). B : predicted MED1 3′-UTR target sites. Bases highlighted in dark gray represent mutations for gene reporter (luciferase) assays. C : normalized luciferase activity in HEK293 cells after dual transfection of miR-96/182/183 mimics and gene (luciferase) reporters harboring putative target sites for miR-96-5p, miR-182-5p, and/or miR-183-5p; n = 4. D : miR-96-5p, miR-182-5p, and miR-183-5p levels in Huh7 cells transfected with 50 nM miR-96-5p, miR-182-5p, and miR-183-5p mimics individually or in combination; real-time PCR; n = 6. E : MED1 mRNA levels in Huh7 cells transfected with 50 nM miR-96-5p, miR-182-5p, and miR-183-5p mimics individually or in combination; real-time PCR; n = 6. F : miR-96-5p, miR-182-5p, and miR-183-5p levels in Huh7 cells transfected with mock or 50 nM locked-nucleic acids (LNAs) against miR-182-5p and/or miR-183-5p; real-time PCR; n = 6. G : MED1 mRNA levels in Huh7 cells transfected mock or 50 nM LNAs against miR-182-5p and/or miR-183-5p; real-time PCR; n = 6. H : protein levels of Med1 and β-actin (loading control) from protein lysates of Huh7 cells transfected with mock or 50 nM miR-96, miR-182, and miR-183 LNAs. Ratio of Med1/β-actin densitometry is indicated between the blots and graphed on the right ; n = 6. A.U. arbitrary units. For comparisons between more than 2 groups to mock only, one-way ANOVA with Bonferonni’s posttest was used, α = 0.05. For comparisons between 2 groups, Mann-Whitney nonparametric tests were used.

    Article Snippet: Real-time PCR was completed with Universal PCR Master Mix and TaqMan mRNA and miRNA assays (ThermoFisher).

    Techniques: Luciferase, Activity Assay, Transfection, Real-time Polymerase Chain Reaction, MANN-WHITNEY

    Bodywide evaluation of the expression of the engineered galactosylceramidase and the biodistribution of the AAV9 vector. (A) Western blot evaluation of the engineered galactosylceramidase from three AAV-treated twitcher mice. Flag tag marks the location of the engineered galactosylceramidase (81 kDa). Alpha-tubulin (50 kDa) is used as the loading control. (B) TaqMan PCR quantification of the AAV9 genome copy number in various tissues. Gas, gastrocnemius muscle; TA, tibialis anterior muscle.

    Journal: Human Gene Therapy

    Article Title: An Engineered Galactosylceramidase Construct Improves AAV Gene Therapy for Krabbe Disease in Twitcher Mice

    doi: 10.1089/hum.2019.008

    Figure Lengend Snippet: Bodywide evaluation of the expression of the engineered galactosylceramidase and the biodistribution of the AAV9 vector. (A) Western blot evaluation of the engineered galactosylceramidase from three AAV-treated twitcher mice. Flag tag marks the location of the engineered galactosylceramidase (81 kDa). Alpha-tubulin (50 kDa) is used as the loading control. (B) TaqMan PCR quantification of the AAV9 genome copy number in various tissues. Gas, gastrocnemius muscle; TA, tibialis anterior muscle.

    Article Snippet: The AAV genome copy number was determined by TaqMan qPCR using the TaqMan Universal PCR Master Mix (Thermo Fisher Scientific).

    Techniques: Expressing, Plasmid Preparation, Western Blot, Mouse Assay, FLAG-tag, Polymerase Chain Reaction

    Effects of aliskiren on myocardial matrix gene expression. Real time PCR was performed with ventricular tissue obtained from mice after 12-inducing diet and different doses of aliskiren. Figure 3A demonstrates changes in expression of COL1A1(alpha 1 chain of type I collagen) and 3B shows changes in COL1A2(alpha2 chain of type I collagen) genes. Lower right panels (3C and 3D) demonstrate the results of western blotting for collagen type I in various groups. Hhe – Hhe-inducing diet; AL 0.5– aliskiren 0.5 mg/kg/day; AL 5– aliskiren 5 mg/kg/day; and AL 50– aliskiren 50 mg/kg/day. * p

    Journal: PLoS ONE

    Article Title: Effects of Direct Renin Inhibition on Myocardial Fibrosis and Cardiac Fibroblast Function

    doi: 10.1371/journal.pone.0081612

    Figure Lengend Snippet: Effects of aliskiren on myocardial matrix gene expression. Real time PCR was performed with ventricular tissue obtained from mice after 12-inducing diet and different doses of aliskiren. Figure 3A demonstrates changes in expression of COL1A1(alpha 1 chain of type I collagen) and 3B shows changes in COL1A2(alpha2 chain of type I collagen) genes. Lower right panels (3C and 3D) demonstrate the results of western blotting for collagen type I in various groups. Hhe – Hhe-inducing diet; AL 0.5– aliskiren 0.5 mg/kg/day; AL 5– aliskiren 5 mg/kg/day; and AL 50– aliskiren 50 mg/kg/day. * p

    Article Snippet: Real-time PCR was performed using the TaqMan universal PCR mastermix (catalog # 4304437, Applied Biosystems, Foster City, CA) and the TaqMan inventoried FAM labeled Gene Expression assays for alpha 1 chain of type I collagen (COL1A1; catalog # Mm00801666_g1 for mouse, catalog # Rn01463848_m1 for rat), alpha 2 chain of type I collagen (COL1A2; catalog # Mm01165187_m1 for mouse, catalog # Rn00670305_m1 for rat), and alpha 1 chain of type III collagen (COL3A1; catalog # Mm01254476_m1).

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

    Effects of aliskiren on homocysteine-induced matrix expression in cultured cardiac fibroblasts. Fibroblasts were cultured in the presence or absence of D,L, homocysteine 200 µmol/L for 24 hours after pretreatment with varying concentrations of aliskiren (0.1–10 µmol/L). Real time PCR was done to measure relative expression of COLIA2 (alpha 2 chain of type I collagen; A) and COL3A1 (alpha 1 chain of type III collagen; B) genes. Figure 5C demonstrates the results of real time PCR to compare the effects of losartan and captopril with aliskiren on homocysteine induced expression of COL1A2 gene. Western blotting was conducted to measure the expression of collagen type I protein (D and E) Glyceraldehyde 3 phosphate dehydrogenase (GAPDH) was used as internal control. Hcy-D,L, homocysteine; AL-aliskiren; Los – losartan; and Cap – captopril. *p

    Journal: PLoS ONE

    Article Title: Effects of Direct Renin Inhibition on Myocardial Fibrosis and Cardiac Fibroblast Function

    doi: 10.1371/journal.pone.0081612

    Figure Lengend Snippet: Effects of aliskiren on homocysteine-induced matrix expression in cultured cardiac fibroblasts. Fibroblasts were cultured in the presence or absence of D,L, homocysteine 200 µmol/L for 24 hours after pretreatment with varying concentrations of aliskiren (0.1–10 µmol/L). Real time PCR was done to measure relative expression of COLIA2 (alpha 2 chain of type I collagen; A) and COL3A1 (alpha 1 chain of type III collagen; B) genes. Figure 5C demonstrates the results of real time PCR to compare the effects of losartan and captopril with aliskiren on homocysteine induced expression of COL1A2 gene. Western blotting was conducted to measure the expression of collagen type I protein (D and E) Glyceraldehyde 3 phosphate dehydrogenase (GAPDH) was used as internal control. Hcy-D,L, homocysteine; AL-aliskiren; Los – losartan; and Cap – captopril. *p

    Article Snippet: Real-time PCR was performed using the TaqMan universal PCR mastermix (catalog # 4304437, Applied Biosystems, Foster City, CA) and the TaqMan inventoried FAM labeled Gene Expression assays for alpha 1 chain of type I collagen (COL1A1; catalog # Mm00801666_g1 for mouse, catalog # Rn01463848_m1 for rat), alpha 2 chain of type I collagen (COL1A2; catalog # Mm01165187_m1 for mouse, catalog # Rn00670305_m1 for rat), and alpha 1 chain of type III collagen (COL3A1; catalog # Mm01254476_m1).

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

    Dysregulation of miR-125b and miR-22 expression in RNA extracted from prostate tissue samples by LCM. (A) Frozen prostate samples were dissected via LCM into benign glandular epithelial versus tumor. Total RNA was extracted using the PicoPure RNA extraction method, as described in Materials and Methods. qRT-PCR was performed with specific primers against miR-125b and miR-22 using the TaqMan ® Universal Master Mix II. C T values were normalized to RNU48 and reported as fold differences compared to benign tissue using the ΔΔCT method of Livak et al. [ 23 ]. Results are the average from frozen tissue samples (n = 4) repeated in 3 technical replicates. (B) From 10 successive slides of a single FFPE prostate sample, miR-125b was quantitated by qRT-PCR as described in panel A for RNA extracted from stroma, benign glandular tissue, BPH, PIN and tumor of stage G4.

    Journal: PLoS ONE

    Article Title: Dual Action of miR-125b As a Tumor Suppressor and OncomiR-22 Promotes Prostate Cancer Tumorigenesis

    doi: 10.1371/journal.pone.0142373

    Figure Lengend Snippet: Dysregulation of miR-125b and miR-22 expression in RNA extracted from prostate tissue samples by LCM. (A) Frozen prostate samples were dissected via LCM into benign glandular epithelial versus tumor. Total RNA was extracted using the PicoPure RNA extraction method, as described in Materials and Methods. qRT-PCR was performed with specific primers against miR-125b and miR-22 using the TaqMan ® Universal Master Mix II. C T values were normalized to RNU48 and reported as fold differences compared to benign tissue using the ΔΔCT method of Livak et al. [ 23 ]. Results are the average from frozen tissue samples (n = 4) repeated in 3 technical replicates. (B) From 10 successive slides of a single FFPE prostate sample, miR-125b was quantitated by qRT-PCR as described in panel A for RNA extracted from stroma, benign glandular tissue, BPH, PIN and tumor of stage G4.

    Article Snippet: Each individual assay was performed in a 20 μl reaction volume with 1.33 μl of cDNA, 1.0 μl specific miR assay, 10 μl TaqMan™ Universal PCR Master Mix II with no AmpErase UNG and 7.67 μl of nuclease free water.

    Techniques: Expressing, Laser Capture Microdissection, RNA Extraction, Quantitative RT-PCR, Formalin-fixed Paraffin-Embedded