Structured Review

Bio-Rad pcr mixture
Inhibition of vaccinia virus transcription by Tkip and SOCS1-KIR. BSC-40 cells mock treated or treated with lipo-Tkip, lipo-SOCS1-KIR, or alanine substitution-containing control peptides for 1 h were infected with vaccinia virus at an MOI of 5 for 1 h. The cells were washed and incubated in growth medium containing the same concentration of peptides for 18 h. RNA was extracted and used for <t>cDNA</t> synthesis, followed by quantitative <t>PCR.</t> The expression of early (D12L) (a), intermediate (AIL) (b), and late (A7L) (c) genes was compared with endogenous actin gene expression.
Pcr Mixture, supplied by Bio-Rad, used in various techniques. Bioz Stars score: 99/100, based on 237 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/pcr mixture/product/Bio-Rad
Average 99 stars, based on 237 article reviews
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pcr mixture - by Bioz Stars, 2021-01
99/100 stars

Images

1) Product Images from "SOCS-1 Mimetics Protect Mice against Lethal Poxvirus Infection: Identification of a Novel Endogenous Antiviral System ▿"

Article Title: SOCS-1 Mimetics Protect Mice against Lethal Poxvirus Infection: Identification of a Novel Endogenous Antiviral System ▿

Journal: Journal of Virology

doi: 10.1128/JVI.01138-08

Inhibition of vaccinia virus transcription by Tkip and SOCS1-KIR. BSC-40 cells mock treated or treated with lipo-Tkip, lipo-SOCS1-KIR, or alanine substitution-containing control peptides for 1 h were infected with vaccinia virus at an MOI of 5 for 1 h. The cells were washed and incubated in growth medium containing the same concentration of peptides for 18 h. RNA was extracted and used for cDNA synthesis, followed by quantitative PCR. The expression of early (D12L) (a), intermediate (AIL) (b), and late (A7L) (c) genes was compared with endogenous actin gene expression.
Figure Legend Snippet: Inhibition of vaccinia virus transcription by Tkip and SOCS1-KIR. BSC-40 cells mock treated or treated with lipo-Tkip, lipo-SOCS1-KIR, or alanine substitution-containing control peptides for 1 h were infected with vaccinia virus at an MOI of 5 for 1 h. The cells were washed and incubated in growth medium containing the same concentration of peptides for 18 h. RNA was extracted and used for cDNA synthesis, followed by quantitative PCR. The expression of early (D12L) (a), intermediate (AIL) (b), and late (A7L) (c) genes was compared with endogenous actin gene expression.

Techniques Used: Inhibition, Infection, Incubation, Concentration Assay, Real-time Polymerase Chain Reaction, Expressing

2) Product Images from "Rift Valley Fever Virus MP-12 Vaccine Is Fully Attenuated by a Combination of Partial Attenuations in the S, M, and L Segments"

Article Title: Rift Valley Fever Virus MP-12 Vaccine Is Fully Attenuated by a Combination of Partial Attenuations in the S, M, and L Segments

Journal: Journal of Virology

doi: 10.1128/JVI.00135-15

Viral replication and blood clinical chemistry at 3 dpi. Outbred CD1 mice ( n = 3 per group) were challenged with a 1 × 10 3 -PFU dose (i.p.) of parental strain rZH501, phosphate-buffered saline (mock-infected controls), or rZH501 with the U795C (Y259H) or A3564G (R1182G) mutation. At 3 dpi, the mice were euthanized and whole blood, sera, or total RNA from livers or spleens was analyzed. (A) Virus titer determined by plaque assay. The detection limit (10 2 PFU/ml) is shown by a dotted line. (B and C) Viral RNA copy numbers per 1 μg of total RNA in the liver (B) and spleen (C) at 3 dpi were determined by droplet digital PCR using a TaqMan probe detecting the RVFV S segment at the N ORF. (D to F) VetScan comprehensive diagnostic profile (Abaxis) test results for ALT (D), ALP (E), and total bilirubin (F) using heparinized whole-blood samples obtained at 3 dpi. The bars in panels A to F represent means and standard errors. (G) Immunohistochemistry of livers from mice infected with the U795C [Y259H (Gn)] (left) or A3564G [R1182G (Gc)] (right) mutant. Arrows, localization of RVFV N antigens.
Figure Legend Snippet: Viral replication and blood clinical chemistry at 3 dpi. Outbred CD1 mice ( n = 3 per group) were challenged with a 1 × 10 3 -PFU dose (i.p.) of parental strain rZH501, phosphate-buffered saline (mock-infected controls), or rZH501 with the U795C (Y259H) or A3564G (R1182G) mutation. At 3 dpi, the mice were euthanized and whole blood, sera, or total RNA from livers or spleens was analyzed. (A) Virus titer determined by plaque assay. The detection limit (10 2 PFU/ml) is shown by a dotted line. (B and C) Viral RNA copy numbers per 1 μg of total RNA in the liver (B) and spleen (C) at 3 dpi were determined by droplet digital PCR using a TaqMan probe detecting the RVFV S segment at the N ORF. (D to F) VetScan comprehensive diagnostic profile (Abaxis) test results for ALT (D), ALP (E), and total bilirubin (F) using heparinized whole-blood samples obtained at 3 dpi. The bars in panels A to F represent means and standard errors. (G) Immunohistochemistry of livers from mice infected with the U795C [Y259H (Gn)] (left) or A3564G [R1182G (Gc)] (right) mutant. Arrows, localization of RVFV N antigens.

Techniques Used: Mouse Assay, Infection, Mutagenesis, Plaque Assay, Digital PCR, Diagnostic Assay, ALP Assay, Immunohistochemistry

3) Product Images from "Detection and genotyping of Helicobacter pylori in saliva versus stool samples from asymptomatic individuals in Northeastern Thailand reveals intra-host tissue-specific H. pylori subtypes"

Article Title: Detection and genotyping of Helicobacter pylori in saliva versus stool samples from asymptomatic individuals in Northeastern Thailand reveals intra-host tissue-specific H. pylori subtypes

Journal: BMC Microbiology

doi: 10.1186/s12866-018-1150-7

Detection of H. pylori directly from stool samples using IFA, semi-nested PCR targeting vac A and real-time PCR targeting 16S rRNA. (A) Fluorescent photomicrograph of H. pylori in various concentrations (CFUs/0.1 g), NC and PC refers to negative (sterile Brucella broth) and positive control ( H. pylori DMST 20165 in Brucella broth), respectively. (B) Semi-nested PCR targeting vac A in spiked stool samples. Lane M, 1 kb DNA ladder; Lane 1, negative control (PCR reagent without DNA); Lane 2, positive control (DNA sample from H. pylori DMST20165); Lanes 3–11, stool samples spiked with various numbers of H. pylori cells (10 8 –10 0 CFUs/0.1 g). (C) Amplification curve of SYBR green real-time PCR targeting 16S rRNA in spiked stool samples. Black line, positive control (DNA sample from H. pylori DMST20165); Red line, 10 6 ; orange line, 10 4 ; blue line, 10 3 ; purple line, 10 1 CFUs/0.1 g; grey line, Non-template control (PCR reagent without DNA)
Figure Legend Snippet: Detection of H. pylori directly from stool samples using IFA, semi-nested PCR targeting vac A and real-time PCR targeting 16S rRNA. (A) Fluorescent photomicrograph of H. pylori in various concentrations (CFUs/0.1 g), NC and PC refers to negative (sterile Brucella broth) and positive control ( H. pylori DMST 20165 in Brucella broth), respectively. (B) Semi-nested PCR targeting vac A in spiked stool samples. Lane M, 1 kb DNA ladder; Lane 1, negative control (PCR reagent without DNA); Lane 2, positive control (DNA sample from H. pylori DMST20165); Lanes 3–11, stool samples spiked with various numbers of H. pylori cells (10 8 –10 0 CFUs/0.1 g). (C) Amplification curve of SYBR green real-time PCR targeting 16S rRNA in spiked stool samples. Black line, positive control (DNA sample from H. pylori DMST20165); Red line, 10 6 ; orange line, 10 4 ; blue line, 10 3 ; purple line, 10 1 CFUs/0.1 g; grey line, Non-template control (PCR reagent without DNA)

Techniques Used: Immunofluorescence, Nested PCR, Real-time Polymerase Chain Reaction, Positive Control, Negative Control, Polymerase Chain Reaction, Amplification, SYBR Green Assay

4) Product Images from "CYP2C19*2, CYP2C19*17 and ITGB3 (PlA1/A2) polymorphisms and resulting therapeutic alterations of clopidogrel and aspirin: A clinical screening among CVD patients who undergone PCI"

Article Title: CYP2C19*2, CYP2C19*17 and ITGB3 (PlA1/A2) polymorphisms and resulting therapeutic alterations of clopidogrel and aspirin: A clinical screening among CVD patients who undergone PCI

Journal: bioRxiv

doi: 10.1101/2020.10.04.325258

T-ARMS- PCR based genotyping of the ITGB3 gene (Lane 1 heterozygous; lane 2,3 normal and lane 4 DNA ladder)
Figure Legend Snippet: T-ARMS- PCR based genotyping of the ITGB3 gene (Lane 1 heterozygous; lane 2,3 normal and lane 4 DNA ladder)

Techniques Used: Polymerase Chain Reaction

Related Articles

Real-time Polymerase Chain Reaction:

Article Title: A combinatorial F box protein directed pathway controls TRAF adaptor stability to regulate inflammation
Article Snippet: .. 10 ng genomic DNA (11.25 μl), 12.5 μl of Taqman Universal PCR master mix and 1.25 μl of SNP genotyping assay were added to optical reaction plates followed by real-time PCR and results were analyzed using CFX manager software (BioRad). ..

Article Title: Neurotrophin Signaling via TrkB and TrkC Receptors Promotes the Growth of Brain Tumor-initiating Cells *
Article Snippet: .. Quantitative PCR for TrkA expression was performed with real time PCR detection system (Bio-Rad) using cDNA, SYBR green PCR master mix (Applied Biosystem, catalog no. 4309155), and primers for TrkA (Qiagen, catalog no. QT00054110, , 112 bp) and actin (Qiagen, catalog no. QT01680476, , 104 bp), and expression was calculated as ΔΔCt, which is normalized to actin. .. Lentiviral plasmids (pLKO.1) containing shRNA sequences to TrkB and TrkC and a nontargeting sequences were obtained from Sigma.

Amplification:

Article Title: Human Traumatic Brain Injury Alters Plasma microRNA Levels
Article Snippet: .. Quantification was performed in a 20-μL reaction containing: 10 μL 2× TaqMan Universal PCR Master Mix, No AmpErase® UNG, 1 μL 20× miRNA-specific primers, 1.33 μL cDNA reaction, and 7.67 μL H2 O. Amplification reactions were performed in an iCycler (BioRad, Hercules, CA) programmed for one cycle of 10 min at 95°C, followed by 50 cycles of 15 sec at 95°C and 1 min at 60°C. .. The resulting data were analyzed using the iCycler iQ optical system software version 3.1 (BioRad).

Size-exclusion Chromatography:

Article Title: Human Traumatic Brain Injury Alters Plasma microRNA Levels
Article Snippet: .. Quantification was performed in a 20-μL reaction containing: 10 μL 2× TaqMan Universal PCR Master Mix, No AmpErase® UNG, 1 μL 20× miRNA-specific primers, 1.33 μL cDNA reaction, and 7.67 μL H2 O. Amplification reactions were performed in an iCycler (BioRad, Hercules, CA) programmed for one cycle of 10 min at 95°C, followed by 50 cycles of 15 sec at 95°C and 1 min at 60°C. .. The resulting data were analyzed using the iCycler iQ optical system software version 3.1 (BioRad).

Quantitative RT-PCR:

Article Title: Transcriptional Analysis of the MrpJ Network: Modulation of Diverse Virulence-Associated Genes and Direct Regulation of mrp Fimbrial and flhDC Flagellar Operons in Proteus mirabilis
Article Snippet: .. Quantitative reverse transcriptase PCR (qRT-PCR) was performed as previously described , with two modifications: the 2× PCR master mix was either SsoAdvanced Universal SYBR green (Bio-Rad; microarray validation) or Maxima SYBR green (Thermo Scientific; ChIP validation), and the thermal cycler was a CFX Connect real-time system (Bio-Rad). .. The 5′ rapid amplification of cDNA ends (5′ RACE) system (Life Technologies) was used to identify the transcriptional start site for the mrpABCDEFGHJ and flhDC operons according to the manufacturer's protocol.

SYBR Green Assay:

Article Title: Transcriptional Analysis of the MrpJ Network: Modulation of Diverse Virulence-Associated Genes and Direct Regulation of mrp Fimbrial and flhDC Flagellar Operons in Proteus mirabilis
Article Snippet: .. Quantitative reverse transcriptase PCR (qRT-PCR) was performed as previously described , with two modifications: the 2× PCR master mix was either SsoAdvanced Universal SYBR green (Bio-Rad; microarray validation) or Maxima SYBR green (Thermo Scientific; ChIP validation), and the thermal cycler was a CFX Connect real-time system (Bio-Rad). .. The 5′ rapid amplification of cDNA ends (5′ RACE) system (Life Technologies) was used to identify the transcriptional start site for the mrpABCDEFGHJ and flhDC operons according to the manufacturer's protocol.

Article Title: Neurotrophin Signaling via TrkB and TrkC Receptors Promotes the Growth of Brain Tumor-initiating Cells *
Article Snippet: .. Quantitative PCR for TrkA expression was performed with real time PCR detection system (Bio-Rad) using cDNA, SYBR green PCR master mix (Applied Biosystem, catalog no. 4309155), and primers for TrkA (Qiagen, catalog no. QT00054110, , 112 bp) and actin (Qiagen, catalog no. QT01680476, , 104 bp), and expression was calculated as ΔΔCt, which is normalized to actin. .. Lentiviral plasmids (pLKO.1) containing shRNA sequences to TrkB and TrkC and a nontargeting sequences were obtained from Sigma.

Microarray:

Article Title: Transcriptional Analysis of the MrpJ Network: Modulation of Diverse Virulence-Associated Genes and Direct Regulation of mrp Fimbrial and flhDC Flagellar Operons in Proteus mirabilis
Article Snippet: .. Quantitative reverse transcriptase PCR (qRT-PCR) was performed as previously described , with two modifications: the 2× PCR master mix was either SsoAdvanced Universal SYBR green (Bio-Rad; microarray validation) or Maxima SYBR green (Thermo Scientific; ChIP validation), and the thermal cycler was a CFX Connect real-time system (Bio-Rad). .. The 5′ rapid amplification of cDNA ends (5′ RACE) system (Life Technologies) was used to identify the transcriptional start site for the mrpABCDEFGHJ and flhDC operons according to the manufacturer's protocol.

SNP Genotyping Assay:

Article Title: A combinatorial F box protein directed pathway controls TRAF adaptor stability to regulate inflammation
Article Snippet: .. 10 ng genomic DNA (11.25 μl), 12.5 μl of Taqman Universal PCR master mix and 1.25 μl of SNP genotyping assay were added to optical reaction plates followed by real-time PCR and results were analyzed using CFX manager software (BioRad). ..

Expressing:

Article Title: Neurotrophin Signaling via TrkB and TrkC Receptors Promotes the Growth of Brain Tumor-initiating Cells *
Article Snippet: .. Quantitative PCR for TrkA expression was performed with real time PCR detection system (Bio-Rad) using cDNA, SYBR green PCR master mix (Applied Biosystem, catalog no. 4309155), and primers for TrkA (Qiagen, catalog no. QT00054110, , 112 bp) and actin (Qiagen, catalog no. QT01680476, , 104 bp), and expression was calculated as ΔΔCt, which is normalized to actin. .. Lentiviral plasmids (pLKO.1) containing shRNA sequences to TrkB and TrkC and a nontargeting sequences were obtained from Sigma.

Polymerase Chain Reaction:

Article Title: PCR-Activated Cell Sorting for Cultivation-Free Enrichment and Sequencing of Rare Microbes
Article Snippet: .. The bacteria is mixed together with primers, Taqman probe and PCR mix (2X ddPCR MasterMix, Biorad). .. The primers and Taqman probe are used at a working concentration of 1μM and 250nM respectively.

Article Title: Regulation of Plasticity and Fibrogenic Activity of Trabecular Meshwork Cells by Rho GTPase Signaling
Article Snippet: .. For q-PCR, the above prepared single stranded cDNA libraries were used in the PCR master mix consisting of iQSYBR Green Supermix (Bio-Rad, Hercules, CA) and gene specific oligo nucleotides. .. PCR reactions were done in triplicate using the following protocol: 95°C for 2 min followed by 50 cycles of 95°C for 15 seconds, 60°C for 15 seconds, and 72°C for 15 seconds.

Article Title: Human Traumatic Brain Injury Alters Plasma microRNA Levels
Article Snippet: .. Quantification was performed in a 20-μL reaction containing: 10 μL 2× TaqMan Universal PCR Master Mix, No AmpErase® UNG, 1 μL 20× miRNA-specific primers, 1.33 μL cDNA reaction, and 7.67 μL H2 O. Amplification reactions were performed in an iCycler (BioRad, Hercules, CA) programmed for one cycle of 10 min at 95°C, followed by 50 cycles of 15 sec at 95°C and 1 min at 60°C. .. The resulting data were analyzed using the iCycler iQ optical system software version 3.1 (BioRad).

Article Title: A combinatorial F box protein directed pathway controls TRAF adaptor stability to regulate inflammation
Article Snippet: .. 10 ng genomic DNA (11.25 μl), 12.5 μl of Taqman Universal PCR master mix and 1.25 μl of SNP genotyping assay were added to optical reaction plates followed by real-time PCR and results were analyzed using CFX manager software (BioRad). ..

Article Title: Connective Tissue Growth Factor-Mediated Upregulation of Neuromedin U Expression in Trabecular Meshwork Cells and its Role in Homeostasis of Aqueous Humor Outflow
Article Snippet: .. The PCR master mix (iQ supermix; Bio-Rad) consisted of 1 to 2 μL template cDNA in 20 μL reaction, 2× PCR master mix, 10 nM fluorescein calibration dye (Bio-Rad), 1 μL of a 1:1500 dilution of 10,000× nucleic acid dye, iQSYBR Green, and 500 nM each of a gene-specific oligonucleotide pair. .. An extension step was used to measure the increase in fluorescence and melting curves obtained immediately after amplification by increasing temperature in 0.4°C increments from 65°C for 85 cycles of 10 seconds each, analyzed (iCycler software; Bio-Rad).

Article Title: Neurotrophin Signaling via TrkB and TrkC Receptors Promotes the Growth of Brain Tumor-initiating Cells *
Article Snippet: .. Quantitative PCR for TrkA expression was performed with real time PCR detection system (Bio-Rad) using cDNA, SYBR green PCR master mix (Applied Biosystem, catalog no. 4309155), and primers for TrkA (Qiagen, catalog no. QT00054110, , 112 bp) and actin (Qiagen, catalog no. QT01680476, , 104 bp), and expression was calculated as ΔΔCt, which is normalized to actin. .. Lentiviral plasmids (pLKO.1) containing shRNA sequences to TrkB and TrkC and a nontargeting sequences were obtained from Sigma.

Article Title: PCR-activated cell sorting as a general, cultivation-free method for high-throughput identification and enrichment of virus hosts
Article Snippet: .. The viral or bacterial suspensions are mixed with the appropriate primers, TaqMan probes, and PCR mix (2X ddPCR MasterMix, Bio-Rad). ..

Chromatin Immunoprecipitation:

Article Title: Transcriptional Analysis of the MrpJ Network: Modulation of Diverse Virulence-Associated Genes and Direct Regulation of mrp Fimbrial and flhDC Flagellar Operons in Proteus mirabilis
Article Snippet: .. Quantitative reverse transcriptase PCR (qRT-PCR) was performed as previously described , with two modifications: the 2× PCR master mix was either SsoAdvanced Universal SYBR green (Bio-Rad; microarray validation) or Maxima SYBR green (Thermo Scientific; ChIP validation), and the thermal cycler was a CFX Connect real-time system (Bio-Rad). .. The 5′ rapid amplification of cDNA ends (5′ RACE) system (Life Technologies) was used to identify the transcriptional start site for the mrpABCDEFGHJ and flhDC operons according to the manufacturer's protocol.

Software:

Article Title: A combinatorial F box protein directed pathway controls TRAF adaptor stability to regulate inflammation
Article Snippet: .. 10 ng genomic DNA (11.25 μl), 12.5 μl of Taqman Universal PCR master mix and 1.25 μl of SNP genotyping assay were added to optical reaction plates followed by real-time PCR and results were analyzed using CFX manager software (BioRad). ..

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  • 92
    Bio-Rad pcr mix
    Linearity of the BCR-ABL <t>ddPCR</t> method when measuring ERM-AD623 samples within a <t>PCR</t> copy number concentration range of 2.5 cp/μL to 5400 cp/μL. The data points represent the average result for eight replicate measurements, and the vertical error bars represent the associated STD. The horizontal error bars represent the standard uncertainty associated with the certified values of the ERM-AD623 samples.
    Pcr Mix, supplied by Bio-Rad, used in various techniques. Bioz Stars score: 92/100, based on 144 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/pcr mix/product/Bio-Rad
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    91
    Bio-Rad sybr green fast qrt pcr mix
    Evaluation of UPR in the mammary gland involution. a Expression of UPR genes Grp78 , Atf4 , Atf6 , Xbp1 (unspliced form), and Chop / Ddit3 was analyzed by <t>qRT-PCR.</t> Lactating mammary gland (involution 0 h) was used as a control, and the expression of each gene at each time point is presented as fold-change relative to control. The horizontal black bar/arrow shows the involution switch from reversible to irreversible stage, which has occurred by 72 h after forced weaning (A, B). b Western analysis of UPR proteins GRP78, ATF4, ATF6, XBP1 (unspliced form), phospho-eIF2a, and CHOP/DDIT3. The vertical bar indicates the involution 0 h (B, Western blot inset). Results at each time point show average ± SD, n = 3. c GRP78 and d CHOP/DDIT3-specific staining (IHC) at different time points during involution and in virgin control mammary glands. All slides were photographed using Olympus BX 61 microscope and 10× magnification (C, D)
    Sybr Green Fast Qrt Pcr Mix, supplied by Bio-Rad, used in various techniques. Bioz Stars score: 91/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/sybr green fast qrt pcr mix/product/Bio-Rad
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    88
    Bio-Rad qrt pcr mixtures
    Induction of LMO2 mRNA expression by FV is increased when the insulator is removed, and induction of LMO2 mRNA expression by LV is decreased when the insulator is added to the LV LTR. cDNA was generated from LMO2 -modified clones containing FV, LV, FV with no insulator (ins.), and LV with the FV insulator placed in the LTR. LMO2 mRNA expression was determined using <t>qRT-PCR.</t> The Hs001534473_m1 primer-probe set and PPIA endogenous control were used to acquire the data. n = 5, 6, 17, and 9 clones, respectively. The error bars indicate SEM.
    Qrt Pcr Mixtures, supplied by Bio-Rad, used in various techniques. Bioz Stars score: 88/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/qrt pcr mixtures/product/Bio-Rad
    Average 88 stars, based on 7 article reviews
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    qrt pcr mixtures - by Bioz Stars, 2021-01
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    88
    Bio-Rad sybr green pcr master mix bio rad
    <t>SYBR</t> Green fluorescence during real‐time amplification with species specific oligos: (a) A gradual delay in amplification and an increase in C q are apparent, which is consistent with 10‐fold gradual decrease in template concentration. (b) The standard curve representing the dilution series indicated in “A”. The C q signal is titrated from 0.5 fg to 50 pg and shown in the standard curve. The slope indicates high level of polymerase chain reaction efficiency
    Sybr Green Pcr Master Mix Bio Rad, supplied by Bio-Rad, used in various techniques. Bioz Stars score: 88/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/sybr green pcr master mix bio rad/product/Bio-Rad
    Average 88 stars, based on 2 article reviews
    Price from $9.99 to $1999.99
    sybr green pcr master mix bio rad - by Bioz Stars, 2021-01
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    Image Search Results


    Linearity of the BCR-ABL ddPCR method when measuring ERM-AD623 samples within a PCR copy number concentration range of 2.5 cp/μL to 5400 cp/μL. The data points represent the average result for eight replicate measurements, and the vertical error bars represent the associated STD. The horizontal error bars represent the standard uncertainty associated with the certified values of the ERM-AD623 samples.

    Journal: Biomolecular Detection and Quantification

    Article Title: Validation of a digital PCR method for quantification of DNA copy number concentrations by using a certified reference material

    doi: 10.1016/j.bdq.2016.08.002

    Figure Lengend Snippet: Linearity of the BCR-ABL ddPCR method when measuring ERM-AD623 samples within a PCR copy number concentration range of 2.5 cp/μL to 5400 cp/μL. The data points represent the average result for eight replicate measurements, and the vertical error bars represent the associated STD. The horizontal error bars represent the standard uncertainty associated with the certified values of the ERM-AD623 samples.

    Article Snippet: The PCR mix comprised 1 × ddPCR Supermix for Probes (Bio-Rad, cat no. 186-3010), suitable primers and probes, nuclease free water (Promega, cat no. P1193) and the DNA sample.

    Techniques: Polymerase Chain Reaction, Concentration Assay

    A schematic overview of all factors which may contribute to the uncertainty of the measurement results obtained with BCR-ABL ddPCR method as performed in this validation study. C primers/probe : concentration primers and probe, Df sample : dilution factor of sample before addition to PCR mix, Df PCR : dilution factor of sample in the PCR mix, M dil : mass of diluent, M dil+sample : mass of diluent and sample, M premix : mass of pre sample mix, M mix : mass of the PCR mix with sample, V d : volume of the droplets

    Journal: Biomolecular Detection and Quantification

    Article Title: Validation of a digital PCR method for quantification of DNA copy number concentrations by using a certified reference material

    doi: 10.1016/j.bdq.2016.08.002

    Figure Lengend Snippet: A schematic overview of all factors which may contribute to the uncertainty of the measurement results obtained with BCR-ABL ddPCR method as performed in this validation study. C primers/probe : concentration primers and probe, Df sample : dilution factor of sample before addition to PCR mix, Df PCR : dilution factor of sample in the PCR mix, M dil : mass of diluent, M dil+sample : mass of diluent and sample, M premix : mass of pre sample mix, M mix : mass of the PCR mix with sample, V d : volume of the droplets

    Article Snippet: The PCR mix comprised 1 × ddPCR Supermix for Probes (Bio-Rad, cat no. 186-3010), suitable primers and probes, nuclease free water (Promega, cat no. P1193) and the DNA sample.

    Techniques: Concentration Assay, Polymerase Chain Reaction

    The relative STD caused by stochastic effects in relation to the PCR copy number concentration for the ddPCR system. The relative STD resulting from stochastic effects ( s s t o c h a s t i c e f f e c t s , r e l ) consists of two components: the relative STD caused by the stochastic effects when sampling the DNA solution added to the PCR mix ( s s a m p l i n g , r e l ) and the relative standard deviation caused by the stochastic effects of the distribution of the target sequence over the analysed droplets ( s d i s t r i b u t i o n , r e l ). The estimation of the s s a m p l i n g , r e l is based on the Poisson distribution, and the estimation of s d i s t r i b u t i o n , r e l is based on the binominal distribution as described in [29] . T s a m p l e d : the expected number of target sequences sampled, T A : the expected number of target sequences in the analysed droplets, A: number of analysed droplets, P: number of positive droplets.

    Journal: Biomolecular Detection and Quantification

    Article Title: Validation of a digital PCR method for quantification of DNA copy number concentrations by using a certified reference material

    doi: 10.1016/j.bdq.2016.08.002

    Figure Lengend Snippet: The relative STD caused by stochastic effects in relation to the PCR copy number concentration for the ddPCR system. The relative STD resulting from stochastic effects ( s s t o c h a s t i c e f f e c t s , r e l ) consists of two components: the relative STD caused by the stochastic effects when sampling the DNA solution added to the PCR mix ( s s a m p l i n g , r e l ) and the relative standard deviation caused by the stochastic effects of the distribution of the target sequence over the analysed droplets ( s d i s t r i b u t i o n , r e l ). The estimation of the s s a m p l i n g , r e l is based on the Poisson distribution, and the estimation of s d i s t r i b u t i o n , r e l is based on the binominal distribution as described in [29] . T s a m p l e d : the expected number of target sequences sampled, T A : the expected number of target sequences in the analysed droplets, A: number of analysed droplets, P: number of positive droplets.

    Article Snippet: The PCR mix comprised 1 × ddPCR Supermix for Probes (Bio-Rad, cat no. 186-3010), suitable primers and probes, nuclease free water (Promega, cat no. P1193) and the DNA sample.

    Techniques: Polymerase Chain Reaction, Concentration Assay, Sampling, Standard Deviation, Sequencing

    Evaluation of UPR in the mammary gland involution. a Expression of UPR genes Grp78 , Atf4 , Atf6 , Xbp1 (unspliced form), and Chop / Ddit3 was analyzed by qRT-PCR. Lactating mammary gland (involution 0 h) was used as a control, and the expression of each gene at each time point is presented as fold-change relative to control. The horizontal black bar/arrow shows the involution switch from reversible to irreversible stage, which has occurred by 72 h after forced weaning (A, B). b Western analysis of UPR proteins GRP78, ATF4, ATF6, XBP1 (unspliced form), phospho-eIF2a, and CHOP/DDIT3. The vertical bar indicates the involution 0 h (B, Western blot inset). Results at each time point show average ± SD, n = 3. c GRP78 and d CHOP/DDIT3-specific staining (IHC) at different time points during involution and in virgin control mammary glands. All slides were photographed using Olympus BX 61 microscope and 10× magnification (C, D)

    Journal: Cell Death Discovery

    Article Title: Autophagy and unfolded protein response (UPR) regulate mammary gland involution by restraining apoptosis-driven irreversible changes

    doi: 10.1038/s41420-018-0105-y

    Figure Lengend Snippet: Evaluation of UPR in the mammary gland involution. a Expression of UPR genes Grp78 , Atf4 , Atf6 , Xbp1 (unspliced form), and Chop / Ddit3 was analyzed by qRT-PCR. Lactating mammary gland (involution 0 h) was used as a control, and the expression of each gene at each time point is presented as fold-change relative to control. The horizontal black bar/arrow shows the involution switch from reversible to irreversible stage, which has occurred by 72 h after forced weaning (A, B). b Western analysis of UPR proteins GRP78, ATF4, ATF6, XBP1 (unspliced form), phospho-eIF2a, and CHOP/DDIT3. The vertical bar indicates the involution 0 h (B, Western blot inset). Results at each time point show average ± SD, n = 3. c GRP78 and d CHOP/DDIT3-specific staining (IHC) at different time points during involution and in virgin control mammary glands. All slides were photographed using Olympus BX 61 microscope and 10× magnification (C, D)

    Article Snippet: Reactions were performed using Biorad SYBR Green Fast qRT-PCR mix and the ABI real-time PCR detection system.

    Techniques: Expressing, Quantitative RT-PCR, Western Blot, Staining, Immunohistochemistry, Microscopy

    Evaluation of autophagy in the mammary gland involution. a Expression of the autophagy genes Atg7 , Atg12 , Ambra-1 , Beclin-1 , and p62 was analyzed by qRT-PCR. Lactating mammary glands (involution 0 h) were used as controls; the expression of each gene at each time point is presented as fold-change relative to control. b Western analysis of the autophagy proteins BECLIN-1, ATG7, LC3-II, and pAMPK are shown. The horizontal black bars/arrows show the involution switch from reversible to irreversible stage, which has occurred by 72 h after forced weaning (A, B). The vertical bar indicates the involution 0 h (B, Western blot inset). Results at each time point show average ± SD, n = 3. c Autophagy marker, (downregulation of) p62 specific staining (IHC) at different time points during involution and in virgin control mammary glands. d H E staining (upper panel) and autophagy specific LC3-GFP punctate formation (lower panel) in identical involution samples from LC3-GFP transgenic mice. All slides were photographed using Olympus BX 61 microscope and 10× magnification (C, D)

    Journal: Cell Death Discovery

    Article Title: Autophagy and unfolded protein response (UPR) regulate mammary gland involution by restraining apoptosis-driven irreversible changes

    doi: 10.1038/s41420-018-0105-y

    Figure Lengend Snippet: Evaluation of autophagy in the mammary gland involution. a Expression of the autophagy genes Atg7 , Atg12 , Ambra-1 , Beclin-1 , and p62 was analyzed by qRT-PCR. Lactating mammary glands (involution 0 h) were used as controls; the expression of each gene at each time point is presented as fold-change relative to control. b Western analysis of the autophagy proteins BECLIN-1, ATG7, LC3-II, and pAMPK are shown. The horizontal black bars/arrows show the involution switch from reversible to irreversible stage, which has occurred by 72 h after forced weaning (A, B). The vertical bar indicates the involution 0 h (B, Western blot inset). Results at each time point show average ± SD, n = 3. c Autophagy marker, (downregulation of) p62 specific staining (IHC) at different time points during involution and in virgin control mammary glands. d H E staining (upper panel) and autophagy specific LC3-GFP punctate formation (lower panel) in identical involution samples from LC3-GFP transgenic mice. All slides were photographed using Olympus BX 61 microscope and 10× magnification (C, D)

    Article Snippet: Reactions were performed using Biorad SYBR Green Fast qRT-PCR mix and the ABI real-time PCR detection system.

    Techniques: Expressing, Quantitative RT-PCR, Western Blot, Marker, Staining, Immunohistochemistry, Transgenic Assay, Mouse Assay, Microscopy

    Induction of LMO2 mRNA expression by FV is increased when the insulator is removed, and induction of LMO2 mRNA expression by LV is decreased when the insulator is added to the LV LTR. cDNA was generated from LMO2 -modified clones containing FV, LV, FV with no insulator (ins.), and LV with the FV insulator placed in the LTR. LMO2 mRNA expression was determined using qRT-PCR. The Hs001534473_m1 primer-probe set and PPIA endogenous control were used to acquire the data. n = 5, 6, 17, and 9 clones, respectively. The error bars indicate SEM.

    Journal: Journal of Virology

    Article Title: Foamy Virus Vector Carries a Strong Insulator in Its Long Terminal Repeat Which Reduces Its Genotoxic Potential

    doi: 10.1128/JVI.01639-17

    Figure Lengend Snippet: Induction of LMO2 mRNA expression by FV is increased when the insulator is removed, and induction of LMO2 mRNA expression by LV is decreased when the insulator is added to the LV LTR. cDNA was generated from LMO2 -modified clones containing FV, LV, FV with no insulator (ins.), and LV with the FV insulator placed in the LTR. LMO2 mRNA expression was determined using qRT-PCR. The Hs001534473_m1 primer-probe set and PPIA endogenous control were used to acquire the data. n = 5, 6, 17, and 9 clones, respectively. The error bars indicate SEM.

    Article Snippet: For LMO2 transcript variant 1 , the probe-primer sets bridge exons 4 and 5 and exons 5 and 6, respectively. qRT-PCR mixtures were prepared with iTaq Universal Probes Supermix (Bio-Rad, Hercules, CA).

    Techniques: Expressing, Generated, Modification, Clone Assay, Quantitative RT-PCR

    SYBR Green fluorescence during real‐time amplification with species specific oligos: (a) A gradual delay in amplification and an increase in C q are apparent, which is consistent with 10‐fold gradual decrease in template concentration. (b) The standard curve representing the dilution series indicated in “A”. The C q signal is titrated from 0.5 fg to 50 pg and shown in the standard curve. The slope indicates high level of polymerase chain reaction efficiency

    Journal: Clinical and Experimental Dental Research

    Article Title: Multiplex real‐time PCR detection and relative quantification of periodontal pathogens

    doi: 10.1002/cre2.37

    Figure Lengend Snippet: SYBR Green fluorescence during real‐time amplification with species specific oligos: (a) A gradual delay in amplification and an increase in C q are apparent, which is consistent with 10‐fold gradual decrease in template concentration. (b) The standard curve representing the dilution series indicated in “A”. The C q signal is titrated from 0.5 fg to 50 pg and shown in the standard curve. The slope indicates high level of polymerase chain reaction efficiency

    Article Snippet: The reaction mixture (total 25 μL) contained 12.5 μL of 2× SYBR Green PCR master mix (Bio‐Rad) and 150 nmol of forward and reverse oligos and 1.0 μL of plasmid DNA dilutions described previously as template.

    Techniques: SYBR Green Assay, Fluorescence, Amplification, Concentration Assay, Polymerase Chain Reaction