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Eppendorf AG thermocycler
Sensitivity assessment of the LAMP assay for Loa loa using serial dilutions of genomic DNA by the addition of SYBR Green I or by visualization on agarose gel stained with ethidium bromide. (A) Sensitivity assessment performed with a <t>thermocycler.</t> (B) Sensitivity assessment performed with a heating block. Lane Loa: genomic DNA from Loa loa (5 ng); lanes 10 −1 –10 −13 : 10-fold serially dilutions; lanes N, N1, N2, N3: negative controls (no DNA template). Lane M: 50 bp DNA ladder (Molecular weight marker XIII, Roche).
Thermocycler, supplied by Eppendorf AG, used in various techniques. Bioz Stars score: 94/100, based on 611 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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1) Product Images from "Development of a Highly Sensitive Loop-Mediated Isothermal Amplification (LAMP) Method for the Detection of Loa loa"

Article Title: Development of a Highly Sensitive Loop-Mediated Isothermal Amplification (LAMP) Method for the Detection of Loa loa

Journal: PLoS ONE

doi: 10.1371/journal.pone.0094664

Sensitivity assessment of the LAMP assay for Loa loa using serial dilutions of genomic DNA by the addition of SYBR Green I or by visualization on agarose gel stained with ethidium bromide. (A) Sensitivity assessment performed with a thermocycler. (B) Sensitivity assessment performed with a heating block. Lane Loa: genomic DNA from Loa loa (5 ng); lanes 10 −1 –10 −13 : 10-fold serially dilutions; lanes N, N1, N2, N3: negative controls (no DNA template). Lane M: 50 bp DNA ladder (Molecular weight marker XIII, Roche).
Figure Legend Snippet: Sensitivity assessment of the LAMP assay for Loa loa using serial dilutions of genomic DNA by the addition of SYBR Green I or by visualization on agarose gel stained with ethidium bromide. (A) Sensitivity assessment performed with a thermocycler. (B) Sensitivity assessment performed with a heating block. Lane Loa: genomic DNA from Loa loa (5 ng); lanes 10 −1 –10 −13 : 10-fold serially dilutions; lanes N, N1, N2, N3: negative controls (no DNA template). Lane M: 50 bp DNA ladder (Molecular weight marker XIII, Roche).

Techniques Used: Lamp Assay, SYBR Green Assay, Agarose Gel Electrophoresis, Staining, Blocking Assay, Molecular Weight, Marker

Related Articles

Clone Assay:

Article Title: Broadcast Spawning Coral Mussismilia hispida Can Vertically Transfer its Associated Bacterial Core
Article Snippet: .. The reaction was performed in a thermocycler (Mastercycler Gradient, Eppendorf, Hamburg, Germany) with the following conditions: initial denaturing at 94°C for 5 min; 1 cycle at 94°C for 1 min, 56°C for 45 s and 72°C; 29 cycles at 92°C for 1 min, 56°C for 1 min and 72°C for 45 s; and a final extension at 72°C for 10 min. Polymerase chain reaction products were cloned using the pJET 1.2 vector (CloneJET PCR Cloning Kit #K1231, Thermo Scientific) and transformed into Escherichia coli competent cells (Single Step – KRX – Competent Cells, Promega) with the TransformAid Bacterial Transformation Kit (#K2710 Thermo Scientific) according to the manufacturer’s instructions. .. Approximately 50 clones were re-amplified for the 28S rRNA gene fragments and digested using the restriction enzyme Taq I (Promega, cutting site 5′T/CGA3′) to perform a screening analysis using RFLPs (Restriction Fragment Length Polymorphisms).

Blocking Assay:

Article Title: Development of a Highly Sensitive Loop-Mediated Isothermal Amplification (LAMP) Method for the Detection of Loa loa
Article Snippet: .. To establish the standard protocol for the LAMP method, the reaction mixture was incubated in a conventional heating block (K Dry-Bath) or in a thermocycler (Mastercycler Gradient-96well; Eppendorf) at a range of temperatures (61, 63 and 65°C) for 60 min to optimize the reaction conditions and then heated at 80°C for 5 min to terminate the reaction. .. Because of the highly sensitivity of LAMP reaction, DNA contamination and carry-over of amplified products were prevented by using sterile tools at all times, performing each step of the analysis in separate work areas, minimizing manipulation of the reaction tubes and closing them with flexible parafilm.

Polymerase Chain Reaction:

Article Title: Broadcast Spawning Coral Mussismilia hispida Can Vertically Transfer its Associated Bacterial Core
Article Snippet: .. The reaction was performed in a thermocycler (Mastercycler Gradient, Eppendorf, Hamburg, Germany) with the following conditions: initial denaturing at 94°C for 5 min; 1 cycle at 94°C for 1 min, 56°C for 45 s and 72°C; 29 cycles at 92°C for 1 min, 56°C for 1 min and 72°C for 45 s; and a final extension at 72°C for 10 min. Polymerase chain reaction products were cloned using the pJET 1.2 vector (CloneJET PCR Cloning Kit #K1231, Thermo Scientific) and transformed into Escherichia coli competent cells (Single Step – KRX – Competent Cells, Promega) with the TransformAid Bacterial Transformation Kit (#K2710 Thermo Scientific) according to the manufacturer’s instructions. .. Approximately 50 clones were re-amplified for the 28S rRNA gene fragments and digested using the restriction enzyme Taq I (Promega, cutting site 5′T/CGA3′) to perform a screening analysis using RFLPs (Restriction Fragment Length Polymorphisms).

Article Title: Signaling-Related Mobility Changes in Bacterial Chemotaxis Receptors Revealed by Solid-State NMR
Article Snippet: .. The PCR reactions were done in a thermocycler (Eppendorf Master Cycler personal or BioRad MJ Mini) using reagents from New England Biolabs. .. Plasmids expressing TEV-cleavable His-tagged proteins were constructed for ease of purification and compatibility with the vesicle assembly of His-tagged CF.

Incubation:

Article Title: Development of a Highly Sensitive Loop-Mediated Isothermal Amplification (LAMP) Method for the Detection of Loa loa
Article Snippet: .. To establish the standard protocol for the LAMP method, the reaction mixture was incubated in a conventional heating block (K Dry-Bath) or in a thermocycler (Mastercycler Gradient-96well; Eppendorf) at a range of temperatures (61, 63 and 65°C) for 60 min to optimize the reaction conditions and then heated at 80°C for 5 min to terminate the reaction. .. Because of the highly sensitivity of LAMP reaction, DNA contamination and carry-over of amplified products were prevented by using sterile tools at all times, performing each step of the analysis in separate work areas, minimizing manipulation of the reaction tubes and closing them with flexible parafilm.

Article Title: Mutational Signature of Aristolochic Acid Exposure as Revealed by Whole-Exome Sequencing
Article Snippet: .. After the third wash, beads were resuspended in 200 μl of SureSelect binding buffer. (ii) To bind captured DNA, the entire hybridization mixture described above (29 μl) was transferred directly from the thermocycler to the bead solution and mixed gently; the hybridization mix/bead solution was incubated in an Eppendorf thermomixer at 850 rpm for 30 min at room temperature. (iii) To wash the beads, the supernatant was removed from beads after applying a Dynal magnetic separator, and the beads were resuspended in 500 μl of SureSelect Wash Buffer #1 by mixing on a vortex mixer for 5 s and incubated for 15 min at room temperature. ..

Article Title: Revisiting Meiosis in Sugarcane: Chromosomal Irregularities and the Prevalence of Bivalent Configurations
Article Snippet: .. Slides were denatured/hybridized for 10 min at each temperature (90°C, 48°C, and 38°C) using a thermocycler (5333 Mastercycler® , Eppendorf) and subsequently incubated in a humidity chamber (20 h, 37°C). .. The CENT probe was detected with anti-digoxigenin conjugated to rhodamine (Roche).

other:

Article Title: SpxA1 and SpxA2 Act Coordinately To Fine-Tune Stress Responses and Virulence in Streptococcus pyogenes
Article Snippet: The maximum growth temperature was determined with C medium and incubating multiple 250-μl cultures of each strain indicated in a thermocycler (Mastercycler pro S; Eppendorf, Hauppauge, NY) set at a constant temperature with a 1°C gradient spread over 12 adjacent wells.

Electroporation Bacterial Transformation:

Article Title: Broadcast Spawning Coral Mussismilia hispida Can Vertically Transfer its Associated Bacterial Core
Article Snippet: .. The reaction was performed in a thermocycler (Mastercycler Gradient, Eppendorf, Hamburg, Germany) with the following conditions: initial denaturing at 94°C for 5 min; 1 cycle at 94°C for 1 min, 56°C for 45 s and 72°C; 29 cycles at 92°C for 1 min, 56°C for 1 min and 72°C for 45 s; and a final extension at 72°C for 10 min. Polymerase chain reaction products were cloned using the pJET 1.2 vector (CloneJET PCR Cloning Kit #K1231, Thermo Scientific) and transformed into Escherichia coli competent cells (Single Step – KRX – Competent Cells, Promega) with the TransformAid Bacterial Transformation Kit (#K2710 Thermo Scientific) according to the manufacturer’s instructions. .. Approximately 50 clones were re-amplified for the 28S rRNA gene fragments and digested using the restriction enzyme Taq I (Promega, cutting site 5′T/CGA3′) to perform a screening analysis using RFLPs (Restriction Fragment Length Polymorphisms).

Transformation Assay:

Article Title: Broadcast Spawning Coral Mussismilia hispida Can Vertically Transfer its Associated Bacterial Core
Article Snippet: .. The reaction was performed in a thermocycler (Mastercycler Gradient, Eppendorf, Hamburg, Germany) with the following conditions: initial denaturing at 94°C for 5 min; 1 cycle at 94°C for 1 min, 56°C for 45 s and 72°C; 29 cycles at 92°C for 1 min, 56°C for 1 min and 72°C for 45 s; and a final extension at 72°C for 10 min. Polymerase chain reaction products were cloned using the pJET 1.2 vector (CloneJET PCR Cloning Kit #K1231, Thermo Scientific) and transformed into Escherichia coli competent cells (Single Step – KRX – Competent Cells, Promega) with the TransformAid Bacterial Transformation Kit (#K2710 Thermo Scientific) according to the manufacturer’s instructions. .. Approximately 50 clones were re-amplified for the 28S rRNA gene fragments and digested using the restriction enzyme Taq I (Promega, cutting site 5′T/CGA3′) to perform a screening analysis using RFLPs (Restriction Fragment Length Polymorphisms).

Binding Assay:

Article Title: Mutational Signature of Aristolochic Acid Exposure as Revealed by Whole-Exome Sequencing
Article Snippet: .. After the third wash, beads were resuspended in 200 μl of SureSelect binding buffer. (ii) To bind captured DNA, the entire hybridization mixture described above (29 μl) was transferred directly from the thermocycler to the bead solution and mixed gently; the hybridization mix/bead solution was incubated in an Eppendorf thermomixer at 850 rpm for 30 min at room temperature. (iii) To wash the beads, the supernatant was removed from beads after applying a Dynal magnetic separator, and the beads were resuspended in 500 μl of SureSelect Wash Buffer #1 by mixing on a vortex mixer for 5 s and incubated for 15 min at room temperature. ..

Plasmid Preparation:

Article Title: Broadcast Spawning Coral Mussismilia hispida Can Vertically Transfer its Associated Bacterial Core
Article Snippet: .. The reaction was performed in a thermocycler (Mastercycler Gradient, Eppendorf, Hamburg, Germany) with the following conditions: initial denaturing at 94°C for 5 min; 1 cycle at 94°C for 1 min, 56°C for 45 s and 72°C; 29 cycles at 92°C for 1 min, 56°C for 1 min and 72°C for 45 s; and a final extension at 72°C for 10 min. Polymerase chain reaction products were cloned using the pJET 1.2 vector (CloneJET PCR Cloning Kit #K1231, Thermo Scientific) and transformed into Escherichia coli competent cells (Single Step – KRX – Competent Cells, Promega) with the TransformAid Bacterial Transformation Kit (#K2710 Thermo Scientific) according to the manufacturer’s instructions. .. Approximately 50 clones were re-amplified for the 28S rRNA gene fragments and digested using the restriction enzyme Taq I (Promega, cutting site 5′T/CGA3′) to perform a screening analysis using RFLPs (Restriction Fragment Length Polymorphisms).

Hybridization:

Article Title: Mutational Signature of Aristolochic Acid Exposure as Revealed by Whole-Exome Sequencing
Article Snippet: .. After the third wash, beads were resuspended in 200 μl of SureSelect binding buffer. (ii) To bind captured DNA, the entire hybridization mixture described above (29 μl) was transferred directly from the thermocycler to the bead solution and mixed gently; the hybridization mix/bead solution was incubated in an Eppendorf thermomixer at 850 rpm for 30 min at room temperature. (iii) To wash the beads, the supernatant was removed from beads after applying a Dynal magnetic separator, and the beads were resuspended in 500 μl of SureSelect Wash Buffer #1 by mixing on a vortex mixer for 5 s and incubated for 15 min at room temperature. ..

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    Eppendorf AG conventional thermocycler
    Diagram of the protocol of in situ RT-PCR combined with immunogold labeling for electron microscopy . Schematic diagram of in situ RT-PCR immunogold protocol. Tissue digestion with proteinase K increases the nucleic acid accessibility. After proteinase K treatment, we performed reverse transcription of mRNA to cDNA followed by a polymerase chain reaction with specific primers to amplify the gene of interest. In this step, biotin-labeled nucleotides are added to the PCR mix and incorporated into the reaction product. For this step we used a <t>thermocycler</t> adapted to glass slides. Then, PCR product was fixed with 4% PFA/0.5%GA, followed by immunogold labeling against biotin with gold-conjugated antibodies. After embedding the tissue in epoxy resin with conventional protocols, we obtained ultrathin sections with an ultramicrotome and detected gold particles with electron microscopy.
    Conventional Thermocycler, supplied by Eppendorf AG, used in various techniques. Bioz Stars score: 91/100, based on 613 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/conventional thermocycler/product/Eppendorf AG
    Average 91 stars, based on 613 article reviews
    Price from $9.99 to $1999.99
    conventional thermocycler - by Bioz Stars, 2020-07
    91/100 stars
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    85
    Eppendorf AG thermocycler 2
    Effect of temperature ramp rates . The standard PCR protocol with Phusion HF DNA polymerase and short initial (30 s) and in-cycle (10 s) denaturation times was performed on three different thermocyclers at their respective default temperature ramp settings. Heating and cooling rates were 6°C/s and 4.5°C/s on thermocycler 1 (bright red line), 4°C/s and 3°C/s on <t>thermocycler</t> 2 (purple line) and 2.2°C/s and 2.2°C/s on thermocycler 3 (dark red line).
    Thermocycler 2, supplied by Eppendorf AG, used in various techniques. Bioz Stars score: 85/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/thermocycler 2/product/Eppendorf AG
    Average 85 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    thermocycler 2 - by Bioz Stars, 2020-07
    85/100 stars
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    85
    Eppendorf AG thermocycler 1
    Effect of temperature ramp rates . The standard PCR protocol with Phusion HF DNA polymerase and short initial (30 s) and in-cycle (10 s) denaturation times was performed on three different thermocyclers at their respective default temperature ramp settings. Heating and cooling rates were 6°C/s and 4.5°C/s on <t>thermocycler</t> 1 (bright red line), 4°C/s and 3°C/s on thermocycler 2 (purple line) and 2.2°C/s and 2.2°C/s on thermocycler 3 (dark red line).
    Thermocycler 1, supplied by Eppendorf AG, used in various techniques. Bioz Stars score: 85/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/thermocycler 1/product/Eppendorf AG
    Average 85 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    thermocycler 1 - by Bioz Stars, 2020-07
    85/100 stars
      Buy from Supplier

    Image Search Results


    Diagram of the protocol of in situ RT-PCR combined with immunogold labeling for electron microscopy . Schematic diagram of in situ RT-PCR immunogold protocol. Tissue digestion with proteinase K increases the nucleic acid accessibility. After proteinase K treatment, we performed reverse transcription of mRNA to cDNA followed by a polymerase chain reaction with specific primers to amplify the gene of interest. In this step, biotin-labeled nucleotides are added to the PCR mix and incorporated into the reaction product. For this step we used a thermocycler adapted to glass slides. Then, PCR product was fixed with 4% PFA/0.5%GA, followed by immunogold labeling against biotin with gold-conjugated antibodies. After embedding the tissue in epoxy resin with conventional protocols, we obtained ultrathin sections with an ultramicrotome and detected gold particles with electron microscopy.

    Journal: Frontiers in Cellular Neuroscience

    Article Title: In situ RT-PCR Optimized for Electron Microscopy Allows Description of Subcellular Morphology of Target mRNA-Expressing Cells in the Brain

    doi: 10.3389/fncel.2017.00141

    Figure Lengend Snippet: Diagram of the protocol of in situ RT-PCR combined with immunogold labeling for electron microscopy . Schematic diagram of in situ RT-PCR immunogold protocol. Tissue digestion with proteinase K increases the nucleic acid accessibility. After proteinase K treatment, we performed reverse transcription of mRNA to cDNA followed by a polymerase chain reaction with specific primers to amplify the gene of interest. In this step, biotin-labeled nucleotides are added to the PCR mix and incorporated into the reaction product. For this step we used a thermocycler adapted to glass slides. Then, PCR product was fixed with 4% PFA/0.5%GA, followed by immunogold labeling against biotin with gold-conjugated antibodies. After embedding the tissue in epoxy resin with conventional protocols, we obtained ultrathin sections with an ultramicrotome and detected gold particles with electron microscopy.

    Article Snippet: Polymerase chain reaction A gradient PCR was performed using the primers and mouse striatum cDNA to test distinct melting temperatures (Tm = 56, 58, and 60°C) in a conventional thermocycler (Mastercycler, Eppendorf, Hamburg, Germany).

    Techniques: In Situ, Reverse Transcription Polymerase Chain Reaction, Labeling, Electron Microscopy, Polymerase Chain Reaction

    Sensitivity assessment of the LAMP assay for Loa loa using serial dilutions of genomic DNA by the addition of SYBR Green I or by visualization on agarose gel stained with ethidium bromide. (A) Sensitivity assessment performed with a thermocycler. (B) Sensitivity assessment performed with a heating block. Lane Loa: genomic DNA from Loa loa (5 ng); lanes 10 −1 –10 −13 : 10-fold serially dilutions; lanes N, N1, N2, N3: negative controls (no DNA template). Lane M: 50 bp DNA ladder (Molecular weight marker XIII, Roche).

    Journal: PLoS ONE

    Article Title: Development of a Highly Sensitive Loop-Mediated Isothermal Amplification (LAMP) Method for the Detection of Loa loa

    doi: 10.1371/journal.pone.0094664

    Figure Lengend Snippet: Sensitivity assessment of the LAMP assay for Loa loa using serial dilutions of genomic DNA by the addition of SYBR Green I or by visualization on agarose gel stained with ethidium bromide. (A) Sensitivity assessment performed with a thermocycler. (B) Sensitivity assessment performed with a heating block. Lane Loa: genomic DNA from Loa loa (5 ng); lanes 10 −1 –10 −13 : 10-fold serially dilutions; lanes N, N1, N2, N3: negative controls (no DNA template). Lane M: 50 bp DNA ladder (Molecular weight marker XIII, Roche).

    Article Snippet: To establish the standard protocol for the LAMP method, the reaction mixture was incubated in a conventional heating block (K Dry-Bath) or in a thermocycler (Mastercycler Gradient-96well; Eppendorf) at a range of temperatures (61, 63 and 65°C) for 60 min to optimize the reaction conditions and then heated at 80°C for 5 min to terminate the reaction.

    Techniques: Lamp Assay, SYBR Green Assay, Agarose Gel Electrophoresis, Staining, Blocking Assay, Molecular Weight, Marker

    Effect of temperature ramp rates . The standard PCR protocol with Phusion HF DNA polymerase and short initial (30 s) and in-cycle (10 s) denaturation times was performed on three different thermocyclers at their respective default temperature ramp settings. Heating and cooling rates were 6°C/s and 4.5°C/s on thermocycler 1 (bright red line), 4°C/s and 3°C/s on thermocycler 2 (purple line) and 2.2°C/s and 2.2°C/s on thermocycler 3 (dark red line).

    Journal: Genome Biology

    Article Title: Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries

    doi: 10.1186/gb-2011-12-2-r18

    Figure Lengend Snippet: Effect of temperature ramp rates . The standard PCR protocol with Phusion HF DNA polymerase and short initial (30 s) and in-cycle (10 s) denaturation times was performed on three different thermocyclers at their respective default temperature ramp settings. Heating and cooling rates were 6°C/s and 4.5°C/s on thermocycler 1 (bright red line), 4°C/s and 3°C/s on thermocycler 2 (purple line) and 2.2°C/s and 2.2°C/s on thermocycler 3 (dark red line).

    Article Snippet: Thermocycler 2 was an Eppendorf Mastercycler epgradient (no 'S').

    Techniques: Polymerase Chain Reaction

    Effect of temperature ramp rates . The standard PCR protocol with Phusion HF DNA polymerase and short initial (30 s) and in-cycle (10 s) denaturation times was performed on three different thermocyclers at their respective default temperature ramp settings. Heating and cooling rates were 6°C/s and 4.5°C/s on thermocycler 1 (bright red line), 4°C/s and 3°C/s on thermocycler 2 (purple line) and 2.2°C/s and 2.2°C/s on thermocycler 3 (dark red line).

    Journal: Genome Biology

    Article Title: Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries

    doi: 10.1186/gb-2011-12-2-r18

    Figure Lengend Snippet: Effect of temperature ramp rates . The standard PCR protocol with Phusion HF DNA polymerase and short initial (30 s) and in-cycle (10 s) denaturation times was performed on three different thermocyclers at their respective default temperature ramp settings. Heating and cooling rates were 6°C/s and 4.5°C/s on thermocycler 1 (bright red line), 4°C/s and 3°C/s on thermocycler 2 (purple line) and 2.2°C/s and 2.2°C/s on thermocycler 3 (dark red line).

    Article Snippet: Thermocycler 1 was a Mastercycler epgradient S (Eppendorf, Hamburg, Germany).

    Techniques: Polymerase Chain Reaction

    Optimized PCR conditions rescue GC-rich promoter regions in the human genome .  (a,b)  A 180-bp fragment library of human DNA was amplified using (a) standard conditions (Phusion HF, short denaturation) or (b) optimized conditions (AccuPrime HiFi, long denaturation, extension at 65°C) on the fast-ramping thermocycler 1. The amplified libraries were analyzed by qPCR. Orange bars indicate the quantity of eight GC-rich loci near gene promoters relative to the mean quantity of four size-matched control loci (blue bars; mean set to 100% in each graph). Error bars represent the range of two measurements averaged to calculate the quantity of each locus. Locus 7 is the first protein-coding exon of the tumor suppressor gene  RB1 .

    Journal: Genome Biology

    Article Title: Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries

    doi: 10.1186/gb-2011-12-2-r18

    Figure Lengend Snippet: Optimized PCR conditions rescue GC-rich promoter regions in the human genome . (a,b) A 180-bp fragment library of human DNA was amplified using (a) standard conditions (Phusion HF, short denaturation) or (b) optimized conditions (AccuPrime HiFi, long denaturation, extension at 65°C) on the fast-ramping thermocycler 1. The amplified libraries were analyzed by qPCR. Orange bars indicate the quantity of eight GC-rich loci near gene promoters relative to the mean quantity of four size-matched control loci (blue bars; mean set to 100% in each graph). Error bars represent the range of two measurements averaged to calculate the quantity of each locus. Locus 7 is the first protein-coding exon of the tumor suppressor gene RB1 .

    Article Snippet: Thermocycler 1 was a Mastercycler epgradient S (Eppendorf, Hamburg, Germany).

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