7500 fast real time pcr system  (Thermo Fisher)


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    Name:
    7500 Real Time PCR System
    Description:
    The 7500 Real Time PCR System is a powerful platform for labs requiring superior performance and maximum dye versatility This system is a sophisticated platform for users who require extended capabilities and maximum versatility The 3rd generation platform features an innovative optical system that enhances sensitivity and lets you access a broader range of fluorophores The variable excitation capability allows greater sensitivity for longer wavelength red dyes • Powerful five color platform is calibrated for the broadest range of dyes available FAM ⁄SYBR Green I VIC ⁄JOE NED ⁄ TAMRA ⁄ Cy3 ROX ⁄Texas Red and Cy5 dyes • Specialized optical system enables easy and accurate calibration to new dyes without requiring the addition of new filter sets• Advanced multi componenting algorithm minimizes spectral crosstalk superior for multiplexing• User friendly software includes plate set up wizards multi plate data viewing capabilities and advanced analysis tools to make data processing simple and straightforwardNEW 7500 Software v2 x Now the easy to use StepOne software is available for both the 7500 and 7500 Fast systems with the 7500 Software v2 x upgrade The 7500 Software v2 x incorporates your favorite StepOne Software features such as a variety of plate setup wizards standard curve dilution and master mix recipe calculators QC flags data filters and email notification when a run is finished The 7500 Software v2 x also includes an enhanced Gene Expression Study package and has a variety of new melting curve protocol options including multiple peak detection step and hold temperature control and customizable ramp rates The NEW Gene Expression Study package accommodates large studies better than any other instrument software package • Import an unlimited number of Comparative CT relative quantitation files to one study • Group samples and view data both by technical replicate group and biological replicate group • Use any gene s as an endogenous control including averaging multiple controls together • Enter known efficiency values to be factored into the RQ results21 CFR Part 11 Module availableThe SDS v1 4 21CFRp11 Module is a powerful tool for assisting with 21CFRp11 compliance while still offering the flexibility of user customizable configuration settings • Individual user log ins can be added for up to four user groups each group with designated permission settings • User customizable permission settings include fourteen system activities e signature authority designation and additional security settings to give you maximum control over your compliance efforts • Audit trails can be enabled or disabled depending on your traceability needs • A selection of e signatures is available to ease e signatures into your workflow Supports Many ApplicationsApplications include gene expression analysis pathogen quantitation SNP genotyping isothermal and ⁄ assays utilizing internal positive controls To facilitate many of these applications Applied Biosystems provides preformulated ready to use quality tested TaqMan assays for use with the 7500 system Now you can reduce your assay optimization efforts Upgrade to High Speed Thermal CyclingAn optional upgrade to the 7500 Fast System is available This 7500 Fast System uses our master mix formulations and enables you to shorten your real time PCR runs to as little as 30 minutes For Research Use Only Not for use in diagnostics procedures
    Catalog Number:
    4351104
    Price:
    None
    Applications:
    Genotyping & Genomic Profiling|PCR & Real-Time PCR|Real Time PCR (qPCR)|Real Time PCR-Based Gene Expression Profiling|Real-Time PCR Instruments, Software & Calibration|Genotyping Instruments, Software & Calibration|Gene Expression Analysis & Genotyping
    Category:
    Instruments and Equipment
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    Structured Review

    Thermo Fisher 7500 fast real time pcr system
    Chemical structure and DNA binding properties of PM01183. (A) Structure of PM01183; (B) binding to naked DNA. Drugs were incubated with a 250 bp <t>PCR</t> product at 25°C during 1 h and the electrophoresis was run in 2% agarose-TAE; (C) relative binding affinities for different DNA triplet sequences. PM01183 was incubated with the labelled double-strand oligodeoxynucleotides at 25°C during 1 h; then the melting assay was started in a <t>7500</t> Fast Real-Time PCR System by increasing the temperature up to 95°C in small steps of 1°C·min −1 . Analysis of the 1/C 50 parameter (drug affinity for specific DNA sequences) and ΔT m (max) (stability of the drug–DNA complex) were analysed with an in-house developed Visual Basic Application (VBA) running on Microsoft Excel. The values correspond to the mean and standard deviation from at least two independent experiments for each sequence.
    The 7500 Real Time PCR System is a powerful platform for labs requiring superior performance and maximum dye versatility This system is a sophisticated platform for users who require extended capabilities and maximum versatility The 3rd generation platform features an innovative optical system that enhances sensitivity and lets you access a broader range of fluorophores The variable excitation capability allows greater sensitivity for longer wavelength red dyes • Powerful five color platform is calibrated for the broadest range of dyes available FAM ⁄SYBR Green I VIC ⁄JOE NED ⁄ TAMRA ⁄ Cy3 ROX ⁄Texas Red and Cy5 dyes • Specialized optical system enables easy and accurate calibration to new dyes without requiring the addition of new filter sets• Advanced multi componenting algorithm minimizes spectral crosstalk superior for multiplexing• User friendly software includes plate set up wizards multi plate data viewing capabilities and advanced analysis tools to make data processing simple and straightforwardNEW 7500 Software v2 x Now the easy to use StepOne software is available for both the 7500 and 7500 Fast systems with the 7500 Software v2 x upgrade The 7500 Software v2 x incorporates your favorite StepOne Software features such as a variety of plate setup wizards standard curve dilution and master mix recipe calculators QC flags data filters and email notification when a run is finished The 7500 Software v2 x also includes an enhanced Gene Expression Study package and has a variety of new melting curve protocol options including multiple peak detection step and hold temperature control and customizable ramp rates The NEW Gene Expression Study package accommodates large studies better than any other instrument software package • Import an unlimited number of Comparative CT relative quantitation files to one study • Group samples and view data both by technical replicate group and biological replicate group • Use any gene s as an endogenous control including averaging multiple controls together • Enter known efficiency values to be factored into the RQ results21 CFR Part 11 Module availableThe SDS v1 4 21CFRp11 Module is a powerful tool for assisting with 21CFRp11 compliance while still offering the flexibility of user customizable configuration settings • Individual user log ins can be added for up to four user groups each group with designated permission settings • User customizable permission settings include fourteen system activities e signature authority designation and additional security settings to give you maximum control over your compliance efforts • Audit trails can be enabled or disabled depending on your traceability needs • A selection of e signatures is available to ease e signatures into your workflow Supports Many ApplicationsApplications include gene expression analysis pathogen quantitation SNP genotyping isothermal and ⁄ assays utilizing internal positive controls To facilitate many of these applications Applied Biosystems provides preformulated ready to use quality tested TaqMan assays for use with the 7500 system Now you can reduce your assay optimization efforts Upgrade to High Speed Thermal CyclingAn optional upgrade to the 7500 Fast System is available This 7500 Fast System uses our master mix formulations and enables you to shorten your real time PCR runs to as little as 30 minutes For Research Use Only Not for use in diagnostics procedures
    https://www.bioz.com/result/7500 fast real time pcr system/product/Thermo Fisher
    Average 99 stars, based on 7768 article reviews
    Price from $9.99 to $1999.99
    7500 fast real time pcr system - by Bioz Stars, 2020-07
    99/100 stars

    Images

    1) Product Images from "PM01183, a new DNA minor groove covalent binder with potent in vitro and in vivo anti-tumour activity"

    Article Title: PM01183, a new DNA minor groove covalent binder with potent in vitro and in vivo anti-tumour activity

    Journal: British Journal of Pharmacology

    doi: 10.1111/j.1476-5381.2010.00945.x

    Chemical structure and DNA binding properties of PM01183. (A) Structure of PM01183; (B) binding to naked DNA. Drugs were incubated with a 250 bp PCR product at 25°C during 1 h and the electrophoresis was run in 2% agarose-TAE; (C) relative binding affinities for different DNA triplet sequences. PM01183 was incubated with the labelled double-strand oligodeoxynucleotides at 25°C during 1 h; then the melting assay was started in a 7500 Fast Real-Time PCR System by increasing the temperature up to 95°C in small steps of 1°C·min −1 . Analysis of the 1/C 50 parameter (drug affinity for specific DNA sequences) and ΔT m (max) (stability of the drug–DNA complex) were analysed with an in-house developed Visual Basic Application (VBA) running on Microsoft Excel. The values correspond to the mean and standard deviation from at least two independent experiments for each sequence.
    Figure Legend Snippet: Chemical structure and DNA binding properties of PM01183. (A) Structure of PM01183; (B) binding to naked DNA. Drugs were incubated with a 250 bp PCR product at 25°C during 1 h and the electrophoresis was run in 2% agarose-TAE; (C) relative binding affinities for different DNA triplet sequences. PM01183 was incubated with the labelled double-strand oligodeoxynucleotides at 25°C during 1 h; then the melting assay was started in a 7500 Fast Real-Time PCR System by increasing the temperature up to 95°C in small steps of 1°C·min −1 . Analysis of the 1/C 50 parameter (drug affinity for specific DNA sequences) and ΔT m (max) (stability of the drug–DNA complex) were analysed with an in-house developed Visual Basic Application (VBA) running on Microsoft Excel. The values correspond to the mean and standard deviation from at least two independent experiments for each sequence.

    Techniques Used: Binding Assay, Incubation, Polymerase Chain Reaction, Electrophoresis, Real-time Polymerase Chain Reaction, Standard Deviation, Sequencing

    2) Product Images from "Upregulation of Mitf by Phenolic Compounds-Rich Cymbopogon schoenanthus Treatment Promotes Melanogenesis in B16 Melanoma Cells and Human Epidermal Melanocytes"

    Article Title: Upregulation of Mitf by Phenolic Compounds-Rich Cymbopogon schoenanthus Treatment Promotes Melanogenesis in B16 Melanoma Cells and Human Epidermal Melanocytes

    Journal: BioMed Research International

    doi: 10.1155/2017/8303671

    Effect of Cymbopogon schoenanthus ethanol extract on the mRNA expression level of melanogenic enzymes: (a) tyrosinase (Tyr) , (b) tyrosinase-related protein 1 (Trp1) , and (c) dopachrome tautomerase (Dct) determined using TaqMan real-time quantitative PCR. B16 cells were cultured in 100 mm dish (3 × 10 6 cells/dish) and treated without (CON) or with 1/1000 (v/v) C. schoenanthus ethanol extract (CYM), using 400 nm alpha-melanocyte-stimulating hormone ( α -MSH) as a positive control and incubated for 4 h after which RNA was extracted, and then reverse transcription PCR was carried out to obtain cDNAs that were used for real-time PCR (ABI 7500 Fast Real-time PCR system). Results represent the mean ± SD of three independent experiments. ∗ Statistically significant ( P ≤ 0.05) difference between control and treated cells.
    Figure Legend Snippet: Effect of Cymbopogon schoenanthus ethanol extract on the mRNA expression level of melanogenic enzymes: (a) tyrosinase (Tyr) , (b) tyrosinase-related protein 1 (Trp1) , and (c) dopachrome tautomerase (Dct) determined using TaqMan real-time quantitative PCR. B16 cells were cultured in 100 mm dish (3 × 10 6 cells/dish) and treated without (CON) or with 1/1000 (v/v) C. schoenanthus ethanol extract (CYM), using 400 nm alpha-melanocyte-stimulating hormone ( α -MSH) as a positive control and incubated for 4 h after which RNA was extracted, and then reverse transcription PCR was carried out to obtain cDNAs that were used for real-time PCR (ABI 7500 Fast Real-time PCR system). Results represent the mean ± SD of three independent experiments. ∗ Statistically significant ( P ≤ 0.05) difference between control and treated cells.

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

    Effect of Cymbopogon schoenanthus ethanol extract on the mRNA expression level of microphthalmia-associated transcription factor (Mitf) determined using TaqMan real-time quantitative PCR. B16 cells were cultured in 100 mm dish (3 × 10 6 cells/dish) and treated without (CON) or with 1/1000 (v/v) C. schoenanthus ethanol extract (CYM), using 400 nm alpha-melanocyte-stimulating hormone ( α -MSH) as a positive control, and incubated for 4 h after which RNA was extracted, and then reverse transcription PCR was carried out to obtain cDNAs that were used for real-time PCR (ABI 7500 Fast Real-time PCR system). Results represent the mean ± SD of three independent experiments. ∗ Statistically significant ( P ≤ 0.05) difference between control and treated cells.
    Figure Legend Snippet: Effect of Cymbopogon schoenanthus ethanol extract on the mRNA expression level of microphthalmia-associated transcription factor (Mitf) determined using TaqMan real-time quantitative PCR. B16 cells were cultured in 100 mm dish (3 × 10 6 cells/dish) and treated without (CON) or with 1/1000 (v/v) C. schoenanthus ethanol extract (CYM), using 400 nm alpha-melanocyte-stimulating hormone ( α -MSH) as a positive control, and incubated for 4 h after which RNA was extracted, and then reverse transcription PCR was carried out to obtain cDNAs that were used for real-time PCR (ABI 7500 Fast Real-time PCR system). Results represent the mean ± SD of three independent experiments. ∗ Statistically significant ( P ≤ 0.05) difference between control and treated cells.

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

    3) Product Images from "Fluorescent Duplex Allele-Specific PCR and Amplicon Melting for Rapid Homogeneous mtDNA Haplogroup H Screening and Sensitive Mixture Detection"

    Article Title: Fluorescent Duplex Allele-Specific PCR and Amplicon Melting for Rapid Homogeneous mtDNA Haplogroup H Screening and Sensitive Mixture Detection

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0008374

    Analytical window of 32-cycle ARMS-DCA for hg H and non-hg H templates. (A, B) Melt-peak data shown originated from an experiment on an ABI PRISM 7700 Sequence Detector. (C, D) Data shown originated from a sensitivity check performed on an Applied Biosystems 7500 Fast Real Time PCR System. Total genomic DNA input amounts are indicated in the panels. For all experiments, 1 pg gDNA equalled approximately 100 mtGE.
    Figure Legend Snippet: Analytical window of 32-cycle ARMS-DCA for hg H and non-hg H templates. (A, B) Melt-peak data shown originated from an experiment on an ABI PRISM 7700 Sequence Detector. (C, D) Data shown originated from a sensitivity check performed on an Applied Biosystems 7500 Fast Real Time PCR System. Total genomic DNA input amounts are indicated in the panels. For all experiments, 1 pg gDNA equalled approximately 100 mtGE.

    Techniques Used: Sequencing, Real-time Polymerase Chain Reaction

    Sensitivity of 7028C/2706G mixture detection depending on the initial amount of template molecules. Data shown originate from two independent 32-cycle ARMS-DCA experiments (800,000–100,000 mtGE and 50,000–6,250 mtGE, n = 1 per mixture ratio/mtDNA input combination) on a 7500 Fast Real Time PCR System. Total template molecule input amounts are given in mtGE, K: ×1000; 1 mtGE equals approximately 10 fg gDNA standard; NTC: no template control.
    Figure Legend Snippet: Sensitivity of 7028C/2706G mixture detection depending on the initial amount of template molecules. Data shown originate from two independent 32-cycle ARMS-DCA experiments (800,000–100,000 mtGE and 50,000–6,250 mtGE, n = 1 per mixture ratio/mtDNA input combination) on a 7500 Fast Real Time PCR System. Total template molecule input amounts are given in mtGE, K: ×1000; 1 mtGE equals approximately 10 fg gDNA standard; NTC: no template control.

    Techniques Used: Real-time Polymerase Chain Reaction

    mtDNA-input dependence of 7028C and 2706G melt ramp heights in pure and admixed hg H and non-hg H samples. The heights of the 7028C and 2706G melt-ramps (Δ F ) were determined from non-normalized melting curves (32-cycle ARMS-DCA; 7500 Fast Real Time PCR System) obtained in two independent 32-cycle ARMS-DCA experiments (800,000–100,000 mtGE and 50,000–6,250 mtGE, singleton data points).
    Figure Legend Snippet: mtDNA-input dependence of 7028C and 2706G melt ramp heights in pure and admixed hg H and non-hg H samples. The heights of the 7028C and 2706G melt-ramps (Δ F ) were determined from non-normalized melting curves (32-cycle ARMS-DCA; 7500 Fast Real Time PCR System) obtained in two independent 32-cycle ARMS-DCA experiments (800,000–100,000 mtGE and 50,000–6,250 mtGE, singleton data points).

    Techniques Used: Real-time Polymerase Chain Reaction

    Influence of the initial copy number and mixture-ratio on the 7028C/2706G melt-ramp height ratio. The ratios of normalized 7028C and 2706G melt-ramp heights (2 independent experiments: 800,000–100,000 mtGE and 50,000–6,250 mtGE, singleton data points, 32-cycle ARMS-DCA; 7500 Fast Real Time PCR System) were visualized as color-coded angles (θ) in degrees.
    Figure Legend Snippet: Influence of the initial copy number and mixture-ratio on the 7028C/2706G melt-ramp height ratio. The ratios of normalized 7028C and 2706G melt-ramp heights (2 independent experiments: 800,000–100,000 mtGE and 50,000–6,250 mtGE, singleton data points, 32-cycle ARMS-DCA; 7500 Fast Real Time PCR System) were visualized as color-coded angles (θ) in degrees.

    Techniques Used: Real-time Polymerase Chain Reaction

    Effects of model inhibitors. Humic acid (A–C) and hematin (D–F) were used as model substances to assess the effects of PCR inhibitors on ARMS-DCA typing of pure and admixed hg H and non-hg-H samples (32-cycle ARMS-DCA, 7500 Fast Real Time PCR System).
    Figure Legend Snippet: Effects of model inhibitors. Humic acid (A–C) and hematin (D–F) were used as model substances to assess the effects of PCR inhibitors on ARMS-DCA typing of pure and admixed hg H and non-hg-H samples (32-cycle ARMS-DCA, 7500 Fast Real Time PCR System).

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

    mtDNA-input dependence of Δ F n and F max , dye translocation, and preferential amplification. (A) The Δ F n and F max data (n = 3, mean ± standard deviation) obtained for an 80% hg H +20% non-hg H mixture originated from two independent 32-cycle ARMS-DCA experiments (800,000 and 600,000 mtGE down to 6,250 and 9,375 mtGE per reaction, respectively, in twofold dilution steps) on a 7500 Fast Real Time PCR System. (B) No template control reactions were used for serially diluting the PCR product (initial template amount in reaction: 800,000 mtGE; 80% hg H +20% non-hg H target-mixture; 32-cycle ARMS-DCA; 7500 Fast Real Time PCR System; data from two independent experiments, n = 5, mean ± standard deviation) to test for amplicon concentration dependent effects on Δ F n 7028C and 2706G. (C) 7028C and 2706G band intensities were determined after polyacrylamide gel-electrophoretic separation of PCR products followed by silver staining (80% hg H +20% non-hg H target-mixture; 32-cycle ARMS-DCA, single experiment, n = 3, mean ± standard deviation).
    Figure Legend Snippet: mtDNA-input dependence of Δ F n and F max , dye translocation, and preferential amplification. (A) The Δ F n and F max data (n = 3, mean ± standard deviation) obtained for an 80% hg H +20% non-hg H mixture originated from two independent 32-cycle ARMS-DCA experiments (800,000 and 600,000 mtGE down to 6,250 and 9,375 mtGE per reaction, respectively, in twofold dilution steps) on a 7500 Fast Real Time PCR System. (B) No template control reactions were used for serially diluting the PCR product (initial template amount in reaction: 800,000 mtGE; 80% hg H +20% non-hg H target-mixture; 32-cycle ARMS-DCA; 7500 Fast Real Time PCR System; data from two independent experiments, n = 5, mean ± standard deviation) to test for amplicon concentration dependent effects on Δ F n 7028C and 2706G. (C) 7028C and 2706G band intensities were determined after polyacrylamide gel-electrophoretic separation of PCR products followed by silver staining (80% hg H +20% non-hg H target-mixture; 32-cycle ARMS-DCA, single experiment, n = 3, mean ± standard deviation).

    Techniques Used: Translocation Assay, Amplification, Standard Deviation, Real-time Polymerase Chain Reaction, Polymerase Chain Reaction, Concentration Assay, Silver Staining

    Mixture ratio resolution and reproducibility of θ values. (A) The ratios of normalized 7028C and 2706G melt-ramp heights (2 independent experiments: 800,000–100,000 mtGE and 50,000–6,250 mtGE, singleton data points, 32-cycle ARMS-DCA; 7500 Fast Real Time PCR System) obtained for pure and admixed hg H and non-hg H templates were transformed into an angle θ and expressed in degrees. Total template molecule input amounts are given in mtGE; K: ×1000. (B) θ values for the selected hg H non-hg H admixtures were obtained with 32-cycle ARMS-DCA (7500 Fast Real Time PCR System; 80% hg H+20% non-hg H: single experiments, n = 3, mean ± standard deviation shown).
    Figure Legend Snippet: Mixture ratio resolution and reproducibility of θ values. (A) The ratios of normalized 7028C and 2706G melt-ramp heights (2 independent experiments: 800,000–100,000 mtGE and 50,000–6,250 mtGE, singleton data points, 32-cycle ARMS-DCA; 7500 Fast Real Time PCR System) obtained for pure and admixed hg H and non-hg H templates were transformed into an angle θ and expressed in degrees. Total template molecule input amounts are given in mtGE; K: ×1000. (B) θ values for the selected hg H non-hg H admixtures were obtained with 32-cycle ARMS-DCA (7500 Fast Real Time PCR System; 80% hg H+20% non-hg H: single experiments, n = 3, mean ± standard deviation shown).

    Techniques Used: Real-time Polymerase Chain Reaction, Transformation Assay, Standard Deviation

    4) Product Images from "Performance Evaluation of the Real-Q Cytomegalovirus (CMV) Quantification Kit Using Two Real-Time PCR Systems for Quantifying CMV DNA in Whole Blood"

    Article Title: Performance Evaluation of the Real-Q Cytomegalovirus (CMV) Quantification Kit Using Two Real-Time PCR Systems for Quantifying CMV DNA in Whole Blood

    Journal: Annals of Laboratory Medicine

    doi: 10.3343/alm.2016.36.6.603

    Bland-Altman plot comparing the artus cytomegalovirus (CMV) RG PCR kit and the Real-Q CMV Quantification kit on different real-time PCR platforms: (A) the 7500 Fast Real-time PCR system, (B) the CFX96 real-time PCR detection system. Solid lines are the mean differences between the values; dashed lines are the mean difference plus or minus 1.96 SD (95% confidential interval of mean difference).
    Figure Legend Snippet: Bland-Altman plot comparing the artus cytomegalovirus (CMV) RG PCR kit and the Real-Q CMV Quantification kit on different real-time PCR platforms: (A) the 7500 Fast Real-time PCR system, (B) the CFX96 real-time PCR detection system. Solid lines are the mean differences between the values; dashed lines are the mean difference plus or minus 1.96 SD (95% confidential interval of mean difference).

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

    Linearity of the Real-Q cytomegalovirus (CMV) Quantification kit on different real-time PCR platforms: (A) the 7500 Fast real-time PCR system and (B) the CFX96 real-time PCR detection system.
    Figure Legend Snippet: Linearity of the Real-Q cytomegalovirus (CMV) Quantification kit on different real-time PCR platforms: (A) the 7500 Fast real-time PCR system and (B) the CFX96 real-time PCR detection system.

    Techniques Used: Real-time Polymerase Chain Reaction

    5) Product Images from "Molecular characterization of a Trichinella spiralis enolase and its interaction with the host’s plasminogen"

    Article Title: Molecular characterization of a Trichinella spiralis enolase and its interaction with the host’s plasminogen

    Journal: Veterinary Research

    doi: 10.1186/s13567-019-0727-y

    Real-time quantitative PCR (qPCR) analysis of Ts- eno transcription at different stages of T. spiralis development. A Agarose gel electrophoresis of the Ts- eno amplicon (188 bp). M: DL2000 DNA marker; 1: NBL; 2: ML; 3: IIL; 4: 3 days AW; 5: 6 days AW. B Agarose gel electrophoresis of the GAPDH amplicon (196 bp). M: DL2000 DNA marker; 1: NBL; 2: ML; 3: IIL; 4: 3 days AW; 5: 6 days AW. C Melt curves of Ts- eno and GAPDH generated by 7500 Software (version 2.0.5). D qPCR analysis of Ts- eno transcription at different T. spiralis stages. The asterisks (*) represent significant differences with other stages ( P
    Figure Legend Snippet: Real-time quantitative PCR (qPCR) analysis of Ts- eno transcription at different stages of T. spiralis development. A Agarose gel electrophoresis of the Ts- eno amplicon (188 bp). M: DL2000 DNA marker; 1: NBL; 2: ML; 3: IIL; 4: 3 days AW; 5: 6 days AW. B Agarose gel electrophoresis of the GAPDH amplicon (196 bp). M: DL2000 DNA marker; 1: NBL; 2: ML; 3: IIL; 4: 3 days AW; 5: 6 days AW. C Melt curves of Ts- eno and GAPDH generated by 7500 Software (version 2.0.5). D qPCR analysis of Ts- eno transcription at different T. spiralis stages. The asterisks (*) represent significant differences with other stages ( P

    Techniques Used: Real-time Polymerase Chain Reaction, Agarose Gel Electrophoresis, Amplification, Marker, Generated, Software

    6) Product Images from "Comprehensive Exploration of Novel Chimeric Transcripts in Clear Cell Renal Cell Carcinomas Using Whole Transcriptome Analysis"

    Article Title: Comprehensive Exploration of Novel Chimeric Transcripts in Clear Cell Renal Cell Carcinomas Using Whole Transcriptome Analysis

    Journal: Genes, Chromosomes & Cancer

    doi: 10.1002/gcc.22211

    Levels of mRNA expression for the partner genes involved in chimeric transcripts in 26 paired samples of tumorous tissue (T) and non-cancerous renal cortex tissue (N) in the second cohort. mRNA expression was analyzed using custom TaqMan Gene Expression Assays on the 7500 Fast Real-Time PCR System (Life Technologies) employing the relative standard curve method. The probes and PCR primer sets used are summarized in Supporting Information Table S6. Experiments were performed in triplicate for each sample-primer set, and the mean value for the three experiments was used as the CT value. All CT values were normalized to that of GAPDH in the same sample. Levels of mRNA expression for the MMACHC, PTER, EPC2, ATXN7, FHIT, KIFAP3, CPEB1, MINPP1, TEX264, FAM107A , UPF3A, CDC16, MCCC1, CPSF3 , and ASAP2 genes were significantly reduced in T samples (shaded column) relative to N samples (white column). Bar, standard deviation.
    Figure Legend Snippet: Levels of mRNA expression for the partner genes involved in chimeric transcripts in 26 paired samples of tumorous tissue (T) and non-cancerous renal cortex tissue (N) in the second cohort. mRNA expression was analyzed using custom TaqMan Gene Expression Assays on the 7500 Fast Real-Time PCR System (Life Technologies) employing the relative standard curve method. The probes and PCR primer sets used are summarized in Supporting Information Table S6. Experiments were performed in triplicate for each sample-primer set, and the mean value for the three experiments was used as the CT value. All CT values were normalized to that of GAPDH in the same sample. Levels of mRNA expression for the MMACHC, PTER, EPC2, ATXN7, FHIT, KIFAP3, CPEB1, MINPP1, TEX264, FAM107A , UPF3A, CDC16, MCCC1, CPSF3 , and ASAP2 genes were significantly reduced in T samples (shaded column) relative to N samples (white column). Bar, standard deviation.

    Techniques Used: Expressing, Real-time Polymerase Chain Reaction, Polymerase Chain Reaction, Standard Deviation

    7) Product Images from "RNAseq Transcriptional Profiling following Whip Development in Sugarcane Smut Disease"

    Article Title: RNAseq Transcriptional Profiling following Whip Development in Sugarcane Smut Disease

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0162237

    RT-qPCR validation. Sugarcane unigenes selected for RT-qPCR analysis of 5-DAI and 200-DAI samples: longifolia-like protein ( comp200950_c0_seq1 ); auxin transporter ( comp205699_c0_seq1 ); SAM ( comp194455_c0_seq1 ); invertase ( comp201528_c0_seq1 ); trehalose 6P synthase ( comp204716_c0_seq1 ); aldolase ( comp196354_c1_seq1 ); pyruvate decarboxylase ( comp200606_c0_seq1 ) andperoxidase ( comp187834_c0_seq1 ). The reactions were performed using a one-step GoTaq ® One-Step RT-qPCR System Kit (Promega) using a 7500 Fast Real-Time PCR System (Applied Biosystems). Statistical analysis was performed using REST ® software. “*” indicates genes differentially expressed in the RT-qPCR reactions (p-value
    Figure Legend Snippet: RT-qPCR validation. Sugarcane unigenes selected for RT-qPCR analysis of 5-DAI and 200-DAI samples: longifolia-like protein ( comp200950_c0_seq1 ); auxin transporter ( comp205699_c0_seq1 ); SAM ( comp194455_c0_seq1 ); invertase ( comp201528_c0_seq1 ); trehalose 6P synthase ( comp204716_c0_seq1 ); aldolase ( comp196354_c1_seq1 ); pyruvate decarboxylase ( comp200606_c0_seq1 ) andperoxidase ( comp187834_c0_seq1 ). The reactions were performed using a one-step GoTaq ® One-Step RT-qPCR System Kit (Promega) using a 7500 Fast Real-Time PCR System (Applied Biosystems). Statistical analysis was performed using REST ® software. “*” indicates genes differentially expressed in the RT-qPCR reactions (p-value

    Techniques Used: Quantitative RT-PCR, Real-time Polymerase Chain Reaction, Software, Significance Assay

    8) Product Images from "Fluorescent Duplex Allele-Specific PCR and Amplicon Melting for Rapid Homogeneous mtDNA Haplogroup H Screening and Sensitive Mixture Detection"

    Article Title: Fluorescent Duplex Allele-Specific PCR and Amplicon Melting for Rapid Homogeneous mtDNA Haplogroup H Screening and Sensitive Mixture Detection

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0008374

    Analytical window of 32-cycle ARMS-DCA for hg H and non-hg H templates. (A, B) Melt-peak data shown originated from an experiment on an ABI PRISM 7700 Sequence Detector. (C, D) Data shown originated from a sensitivity check performed on an Applied Biosystems 7500 Fast Real Time PCR System. Total genomic DNA input amounts are indicated in the panels. For all experiments, 1 pg gDNA equalled approximately 100 mtGE.
    Figure Legend Snippet: Analytical window of 32-cycle ARMS-DCA for hg H and non-hg H templates. (A, B) Melt-peak data shown originated from an experiment on an ABI PRISM 7700 Sequence Detector. (C, D) Data shown originated from a sensitivity check performed on an Applied Biosystems 7500 Fast Real Time PCR System. Total genomic DNA input amounts are indicated in the panels. For all experiments, 1 pg gDNA equalled approximately 100 mtGE.

    Techniques Used: Sequencing, Real-time Polymerase Chain Reaction

    Sensitivity of 7028C/2706G mixture detection depending on the initial amount of template molecules. Data shown originate from two independent 32-cycle ARMS-DCA experiments (800,000–100,000 mtGE and 50,000–6,250 mtGE, n = 1 per mixture ratio/mtDNA input combination) on a 7500 Fast Real Time PCR System. Total template molecule input amounts are given in mtGE, K: ×1000; 1 mtGE equals approximately 10 fg gDNA standard; NTC: no template control.
    Figure Legend Snippet: Sensitivity of 7028C/2706G mixture detection depending on the initial amount of template molecules. Data shown originate from two independent 32-cycle ARMS-DCA experiments (800,000–100,000 mtGE and 50,000–6,250 mtGE, n = 1 per mixture ratio/mtDNA input combination) on a 7500 Fast Real Time PCR System. Total template molecule input amounts are given in mtGE, K: ×1000; 1 mtGE equals approximately 10 fg gDNA standard; NTC: no template control.

    Techniques Used: Real-time Polymerase Chain Reaction

    mtDNA-input dependence of 7028C and 2706G melt ramp heights in pure and admixed hg H and non-hg H samples. The heights of the 7028C and 2706G melt-ramps (Δ F ) were determined from non-normalized melting curves (32-cycle ARMS-DCA; 7500 Fast Real Time PCR System) obtained in two independent 32-cycle ARMS-DCA experiments (800,000–100,000 mtGE and 50,000–6,250 mtGE, singleton data points).
    Figure Legend Snippet: mtDNA-input dependence of 7028C and 2706G melt ramp heights in pure and admixed hg H and non-hg H samples. The heights of the 7028C and 2706G melt-ramps (Δ F ) were determined from non-normalized melting curves (32-cycle ARMS-DCA; 7500 Fast Real Time PCR System) obtained in two independent 32-cycle ARMS-DCA experiments (800,000–100,000 mtGE and 50,000–6,250 mtGE, singleton data points).

    Techniques Used: Real-time Polymerase Chain Reaction

    Influence of the initial copy number and mixture-ratio on the 7028C/2706G melt-ramp height ratio. The ratios of normalized 7028C and 2706G melt-ramp heights (2 independent experiments: 800,000–100,000 mtGE and 50,000–6,250 mtGE, singleton data points, 32-cycle ARMS-DCA; 7500 Fast Real Time PCR System) were visualized as color-coded angles (θ) in degrees.
    Figure Legend Snippet: Influence of the initial copy number and mixture-ratio on the 7028C/2706G melt-ramp height ratio. The ratios of normalized 7028C and 2706G melt-ramp heights (2 independent experiments: 800,000–100,000 mtGE and 50,000–6,250 mtGE, singleton data points, 32-cycle ARMS-DCA; 7500 Fast Real Time PCR System) were visualized as color-coded angles (θ) in degrees.

    Techniques Used: Real-time Polymerase Chain Reaction

    Effects of model inhibitors. Humic acid (A–C) and hematin (D–F) were used as model substances to assess the effects of PCR inhibitors on ARMS-DCA typing of pure and admixed hg H and non-hg-H samples (32-cycle ARMS-DCA, 7500 Fast Real Time PCR System).
    Figure Legend Snippet: Effects of model inhibitors. Humic acid (A–C) and hematin (D–F) were used as model substances to assess the effects of PCR inhibitors on ARMS-DCA typing of pure and admixed hg H and non-hg-H samples (32-cycle ARMS-DCA, 7500 Fast Real Time PCR System).

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

    mtDNA-input dependence of Δ F n and F max , dye translocation, and preferential amplification. (A) The Δ F n and F max data (n = 3, mean ± standard deviation) obtained for an 80% hg H +20% non-hg H mixture originated from two independent 32-cycle ARMS-DCA experiments (800,000 and 600,000 mtGE down to 6,250 and 9,375 mtGE per reaction, respectively, in twofold dilution steps) on a 7500 Fast Real Time PCR System. (B) No template control reactions were used for serially diluting the PCR product (initial template amount in reaction: 800,000 mtGE; 80% hg H +20% non-hg H target-mixture; 32-cycle ARMS-DCA; 7500 Fast Real Time PCR System; data from two independent experiments, n = 5, mean ± standard deviation) to test for amplicon concentration dependent effects on Δ F n 7028C and 2706G. (C) 7028C and 2706G band intensities were determined after polyacrylamide gel-electrophoretic separation of PCR products followed by silver staining (80% hg H +20% non-hg H target-mixture; 32-cycle ARMS-DCA, single experiment, n = 3, mean ± standard deviation).
    Figure Legend Snippet: mtDNA-input dependence of Δ F n and F max , dye translocation, and preferential amplification. (A) The Δ F n and F max data (n = 3, mean ± standard deviation) obtained for an 80% hg H +20% non-hg H mixture originated from two independent 32-cycle ARMS-DCA experiments (800,000 and 600,000 mtGE down to 6,250 and 9,375 mtGE per reaction, respectively, in twofold dilution steps) on a 7500 Fast Real Time PCR System. (B) No template control reactions were used for serially diluting the PCR product (initial template amount in reaction: 800,000 mtGE; 80% hg H +20% non-hg H target-mixture; 32-cycle ARMS-DCA; 7500 Fast Real Time PCR System; data from two independent experiments, n = 5, mean ± standard deviation) to test for amplicon concentration dependent effects on Δ F n 7028C and 2706G. (C) 7028C and 2706G band intensities were determined after polyacrylamide gel-electrophoretic separation of PCR products followed by silver staining (80% hg H +20% non-hg H target-mixture; 32-cycle ARMS-DCA, single experiment, n = 3, mean ± standard deviation).

    Techniques Used: Translocation Assay, Amplification, Standard Deviation, Real-time Polymerase Chain Reaction, Polymerase Chain Reaction, Concentration Assay, Silver Staining

    Mixture ratio resolution and reproducibility of θ values. (A) The ratios of normalized 7028C and 2706G melt-ramp heights (2 independent experiments: 800,000–100,000 mtGE and 50,000–6,250 mtGE, singleton data points, 32-cycle ARMS-DCA; 7500 Fast Real Time PCR System) obtained for pure and admixed hg H and non-hg H templates were transformed into an angle θ and expressed in degrees. Total template molecule input amounts are given in mtGE; K: ×1000. (B) θ values for the selected hg H non-hg H admixtures were obtained with 32-cycle ARMS-DCA (7500 Fast Real Time PCR System; 80% hg H+20% non-hg H: single experiments, n = 3, mean ± standard deviation shown).
    Figure Legend Snippet: Mixture ratio resolution and reproducibility of θ values. (A) The ratios of normalized 7028C and 2706G melt-ramp heights (2 independent experiments: 800,000–100,000 mtGE and 50,000–6,250 mtGE, singleton data points, 32-cycle ARMS-DCA; 7500 Fast Real Time PCR System) obtained for pure and admixed hg H and non-hg H templates were transformed into an angle θ and expressed in degrees. Total template molecule input amounts are given in mtGE; K: ×1000. (B) θ values for the selected hg H non-hg H admixtures were obtained with 32-cycle ARMS-DCA (7500 Fast Real Time PCR System; 80% hg H+20% non-hg H: single experiments, n = 3, mean ± standard deviation shown).

    Techniques Used: Real-time Polymerase Chain Reaction, Transformation Assay, Standard Deviation

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    Amplification:

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    Fluorescence:

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    Quantitative RT-PCR:

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    Article Snippet: .. qRT-PCR Total RNA from hPDL cells and rat upper first molar periodontal tissue samples (n = 4) were extracted using Trizol reagent (Invitrogen, California, USA), and converted to cDNA using a PrimeScript RT reagent Kit (Takara Co., Shiga, Japan). qRT-PCR amplification was performed in a Real-Time PCR System (Applied Biosystems 7500, ABI). .. The primer sequences and PCR product sizes are shown in .

    Real-time Polymerase Chain Reaction:

    Article Title: High incidence of leukemia in large animals after stem cell gene therapy with a HOXB4-expressing retroviral vector
    Article Snippet: .. For quantitative analysis of gene expression, SYBR Green real-time PCR was performed on 7500 Real Time PCR System (Applied Biosystems). ..

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    Polymerase Chain Reaction:

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    Thermo Fisher abi 7500 fast dx
    Analytical performance comparison between Trioplex assay multiplex and the ZIKV singleplex format assay using small volume and large volume RNA extraction. Normal human serum or urine was contrived with ZIKV at a dilution of 1:10 before the limit of detection (1:10 BLoD), at the limit of detection (LoD), and at 1:10 after the limit of detection (1:10 ALoD). Twenty replicates of every dilution were extracted using the MagNA Pure 96 instrument (Roche) and tested by Trioplex assay multiplex or ZIKV singleplex format assay on the <t>ABI</t> 7500 Fast Dx or the QuantStudio Dx instruments. a Compares the mean genome copy equivalents per PCR reaction (GCE/rxn) of viral RNA extracted from serum at each dilution on the ABI 7500 Fast Dx instrument. A linear regression was plotted for multiplex with small volume protocol (Sv) (0.2 mL) (black straight line), singleplex assay with small volume protocol (gray straight line), multiplex with large volume protocol (Lv) (1 mL) (black dashed line). and singleplex assay with large volume protocol (gray dashed line). b Compares the mean genome copy equivalents per PCR reaction (GCE/rxn) of viral RNA extracted from serum or urine at each dilution on the QuantStudio Dx instrument. A linear regression was plotted for multiplex with small volume protocol serum (Sv) (black straight line), multiplex with large volume protocol serum (Lv) (gray straight line), multiplex with small volume protocol urine (Lv) (black dashed line), and multiplex with large volume protocol urine (gray dashed line). Error bars represent GCE/mL standard deviation. The CT values for every dilution replicate in serum tested was plotted for c small volume and d large volume extractions
    Abi 7500 Fast Dx, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 98 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher fast real time pcr system
    Gene expression analysis by RNA sequencing of LT-HSCs and MEPs. (A) Unsupervised clustering of differentially expressed genes (P ≤ 0.05; log2-fold changes > 1.5). Each column represents data from one individual mouse. The color code for the genotypes of the individual mice is the same as in B. (B) PCA. The data for LT-HSCs and MEPs were derived from two independent experiments and combined ( n = 4 or 5 for SclCre , n = 7 or 4 for SclCre;Ezh2 +/Δ , n = 4 for SclCre;Ezh2 Δ/Δ , n = 6 or 4 for SclCre;V617F , n = 8 or 6 SclCre;V617F;Ezh2 +/Δ , and n = 6 for SclCre;V617F;Ezh2 Δ/Δ for LT-HSCs or MEP analysis). Each dot represents data from one individual mouse. (C) Competitive gene set enrichment analysis for gene expression signatures of interferon-γ, interferon-α, and fetal liver HSCs in LT-HSCs of SclCre;V617F;Ezh2 Δ/Δ compared with SclCre;V617F . (D) Plot showing the number of differentially expressed genes with cutoff of P ≤ 0.05. (E) Gene list of top 10 significant gene expression differences according to the absolute fold change. (F) Expression levels of Lin28b and Hmga2 . Each dot represents data from one individual mouse. (G) Relative expression of HMGA2 , IGF2BP3 , and Pcolce2 determined by <t>qPCR</t> in granulocyte RNA from patients with MPN that carry mutations in EZH2 or CALR . Each dot represents data from one individual patient. The mutations in patient granulocyte were determined by allele-specific <t>PCR</t> ( n = 4 for CALR mutation with WT EZH2 , n = 4 for CALR mutation with heterozygous mutation of EZH2 , n = 1 for CALR mutation with homozygous mutation of EZH2 , n = 8 for JAK2V617F mutation with WT EZH2 , n = 12 for JAK2V617F mutation with heterozygous mutation of EZH2 , and n = 4 for JAK2V617F mutation with h homozygous mutation of EZH2 ). (F and G) Horizontal lines indicate the mean of the values. *, P
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    Analytical performance comparison between Trioplex assay multiplex and the ZIKV singleplex format assay using small volume and large volume RNA extraction. Normal human serum or urine was contrived with ZIKV at a dilution of 1:10 before the limit of detection (1:10 BLoD), at the limit of detection (LoD), and at 1:10 after the limit of detection (1:10 ALoD). Twenty replicates of every dilution were extracted using the MagNA Pure 96 instrument (Roche) and tested by Trioplex assay multiplex or ZIKV singleplex format assay on the ABI 7500 Fast Dx or the QuantStudio Dx instruments. a Compares the mean genome copy equivalents per PCR reaction (GCE/rxn) of viral RNA extracted from serum at each dilution on the ABI 7500 Fast Dx instrument. A linear regression was plotted for multiplex with small volume protocol (Sv) (0.2 mL) (black straight line), singleplex assay with small volume protocol (gray straight line), multiplex with large volume protocol (Lv) (1 mL) (black dashed line). and singleplex assay with large volume protocol (gray dashed line). b Compares the mean genome copy equivalents per PCR reaction (GCE/rxn) of viral RNA extracted from serum or urine at each dilution on the QuantStudio Dx instrument. A linear regression was plotted for multiplex with small volume protocol serum (Sv) (black straight line), multiplex with large volume protocol serum (Lv) (gray straight line), multiplex with small volume protocol urine (Lv) (black dashed line), and multiplex with large volume protocol urine (gray dashed line). Error bars represent GCE/mL standard deviation. The CT values for every dilution replicate in serum tested was plotted for c small volume and d large volume extractions

    Journal: Nature Communications

    Article Title: Performance of the Trioplex real-time RT-PCR assay for detection of Zika, dengue, and chikungunya viruses

    doi: 10.1038/s41467-018-03772-1

    Figure Lengend Snippet: Analytical performance comparison between Trioplex assay multiplex and the ZIKV singleplex format assay using small volume and large volume RNA extraction. Normal human serum or urine was contrived with ZIKV at a dilution of 1:10 before the limit of detection (1:10 BLoD), at the limit of detection (LoD), and at 1:10 after the limit of detection (1:10 ALoD). Twenty replicates of every dilution were extracted using the MagNA Pure 96 instrument (Roche) and tested by Trioplex assay multiplex or ZIKV singleplex format assay on the ABI 7500 Fast Dx or the QuantStudio Dx instruments. a Compares the mean genome copy equivalents per PCR reaction (GCE/rxn) of viral RNA extracted from serum at each dilution on the ABI 7500 Fast Dx instrument. A linear regression was plotted for multiplex with small volume protocol (Sv) (0.2 mL) (black straight line), singleplex assay with small volume protocol (gray straight line), multiplex with large volume protocol (Lv) (1 mL) (black dashed line). and singleplex assay with large volume protocol (gray dashed line). b Compares the mean genome copy equivalents per PCR reaction (GCE/rxn) of viral RNA extracted from serum or urine at each dilution on the QuantStudio Dx instrument. A linear regression was plotted for multiplex with small volume protocol serum (Sv) (black straight line), multiplex with large volume protocol serum (Lv) (gray straight line), multiplex with small volume protocol urine (Lv) (black dashed line), and multiplex with large volume protocol urine (gray dashed line). Error bars represent GCE/mL standard deviation. The CT values for every dilution replicate in serum tested was plotted for c small volume and d large volume extractions

    Article Snippet: The performance of an alternative RT-PCR master mix, qScript™ One-Step qRT-PCR kit, Low Rox™ (Quanta) real-time RT-PCR master mix, was evaluated on the ABI 7500 Fast Dx and QuantStudio Dx instruments using the same RNA that was tested in the previous study.

    Techniques: Multiplex Assay, RNA Extraction, Polymerase Chain Reaction, Singleplex Assay, Standard Deviation

    Clinical performance of the Trioplex assay across specimen types. Clinical specimens collected concurrently from 373 cases with previous Zika determination in the acute stage were tested. RNA was extracted with the MagNA Pure 96 small volume external lysis protocol from 373 case-paired serum, 373 urine, and 345 whole blood-EDTA specimens and tested with the Trioplex assay in multiplex format in the ABI 7500 Fast Dx instrument. a Correlation of CT values between case-matching serum and urine specimens; R 2 = 0.36 p

    Journal: Nature Communications

    Article Title: Performance of the Trioplex real-time RT-PCR assay for detection of Zika, dengue, and chikungunya viruses

    doi: 10.1038/s41467-018-03772-1

    Figure Lengend Snippet: Clinical performance of the Trioplex assay across specimen types. Clinical specimens collected concurrently from 373 cases with previous Zika determination in the acute stage were tested. RNA was extracted with the MagNA Pure 96 small volume external lysis protocol from 373 case-paired serum, 373 urine, and 345 whole blood-EDTA specimens and tested with the Trioplex assay in multiplex format in the ABI 7500 Fast Dx instrument. a Correlation of CT values between case-matching serum and urine specimens; R 2 = 0.36 p

    Article Snippet: The performance of an alternative RT-PCR master mix, qScript™ One-Step qRT-PCR kit, Low Rox™ (Quanta) real-time RT-PCR master mix, was evaluated on the ABI 7500 Fast Dx and QuantStudio Dx instruments using the same RNA that was tested in the previous study.

    Techniques: Lysis, Multiplex Assay

    Gene expression analysis by RNA sequencing of LT-HSCs and MEPs. (A) Unsupervised clustering of differentially expressed genes (P ≤ 0.05; log2-fold changes > 1.5). Each column represents data from one individual mouse. The color code for the genotypes of the individual mice is the same as in B. (B) PCA. The data for LT-HSCs and MEPs were derived from two independent experiments and combined ( n = 4 or 5 for SclCre , n = 7 or 4 for SclCre;Ezh2 +/Δ , n = 4 for SclCre;Ezh2 Δ/Δ , n = 6 or 4 for SclCre;V617F , n = 8 or 6 SclCre;V617F;Ezh2 +/Δ , and n = 6 for SclCre;V617F;Ezh2 Δ/Δ for LT-HSCs or MEP analysis). Each dot represents data from one individual mouse. (C) Competitive gene set enrichment analysis for gene expression signatures of interferon-γ, interferon-α, and fetal liver HSCs in LT-HSCs of SclCre;V617F;Ezh2 Δ/Δ compared with SclCre;V617F . (D) Plot showing the number of differentially expressed genes with cutoff of P ≤ 0.05. (E) Gene list of top 10 significant gene expression differences according to the absolute fold change. (F) Expression levels of Lin28b and Hmga2 . Each dot represents data from one individual mouse. (G) Relative expression of HMGA2 , IGF2BP3 , and Pcolce2 determined by qPCR in granulocyte RNA from patients with MPN that carry mutations in EZH2 or CALR . Each dot represents data from one individual patient. The mutations in patient granulocyte were determined by allele-specific PCR ( n = 4 for CALR mutation with WT EZH2 , n = 4 for CALR mutation with heterozygous mutation of EZH2 , n = 1 for CALR mutation with homozygous mutation of EZH2 , n = 8 for JAK2V617F mutation with WT EZH2 , n = 12 for JAK2V617F mutation with heterozygous mutation of EZH2 , and n = 4 for JAK2V617F mutation with h homozygous mutation of EZH2 ). (F and G) Horizontal lines indicate the mean of the values. *, P

    Journal: The Journal of Experimental Medicine

    Article Title: Loss of Ezh2 synergizes with JAK2-V617F in initiating myeloproliferative neoplasms and promoting myelofibrosis

    doi: 10.1084/jem.20151136

    Figure Lengend Snippet: Gene expression analysis by RNA sequencing of LT-HSCs and MEPs. (A) Unsupervised clustering of differentially expressed genes (P ≤ 0.05; log2-fold changes > 1.5). Each column represents data from one individual mouse. The color code for the genotypes of the individual mice is the same as in B. (B) PCA. The data for LT-HSCs and MEPs were derived from two independent experiments and combined ( n = 4 or 5 for SclCre , n = 7 or 4 for SclCre;Ezh2 +/Δ , n = 4 for SclCre;Ezh2 Δ/Δ , n = 6 or 4 for SclCre;V617F , n = 8 or 6 SclCre;V617F;Ezh2 +/Δ , and n = 6 for SclCre;V617F;Ezh2 Δ/Δ for LT-HSCs or MEP analysis). Each dot represents data from one individual mouse. (C) Competitive gene set enrichment analysis for gene expression signatures of interferon-γ, interferon-α, and fetal liver HSCs in LT-HSCs of SclCre;V617F;Ezh2 Δ/Δ compared with SclCre;V617F . (D) Plot showing the number of differentially expressed genes with cutoff of P ≤ 0.05. (E) Gene list of top 10 significant gene expression differences according to the absolute fold change. (F) Expression levels of Lin28b and Hmga2 . Each dot represents data from one individual mouse. (G) Relative expression of HMGA2 , IGF2BP3 , and Pcolce2 determined by qPCR in granulocyte RNA from patients with MPN that carry mutations in EZH2 or CALR . Each dot represents data from one individual patient. The mutations in patient granulocyte were determined by allele-specific PCR ( n = 4 for CALR mutation with WT EZH2 , n = 4 for CALR mutation with heterozygous mutation of EZH2 , n = 1 for CALR mutation with homozygous mutation of EZH2 , n = 8 for JAK2V617F mutation with WT EZH2 , n = 12 for JAK2V617F mutation with heterozygous mutation of EZH2 , and n = 4 for JAK2V617F mutation with h homozygous mutation of EZH2 ). (F and G) Horizontal lines indicate the mean of the values. *, P

    Article Snippet: Real-time qPCR was performed with 7500 Fast Real-Time PCR System, using the TaqMan gene expression system (Thermo Fisher Scientific) and normalized by human GUSB.

    Techniques: Expressing, RNA Sequencing Assay, Mouse Assay, Derivative Assay, Real-time Polymerase Chain Reaction, Polymerase Chain Reaction, Mutagenesis