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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).
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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

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Clone Assay:

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Amplification:

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

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Synthesized:

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Neutralization:

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Blocking Assay:

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Microarray:

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Incubation:

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Article Title: Development of a Highly Sensitive Loop-Mediated Isothermal Amplification (LAMP) Method for the Detection of Loa loa
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Article Title: Arsenic Resistance and Prevalence of Arsenic Resistance Genes in Campylobacter jejuni and Campylobacter coli Isolated from Retail Meats
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Article Title: Mutational Signature of Aristolochic Acid Exposure as Revealed by Whole-Exome Sequencing
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Article Title: Identification of novel Fgf enhancers and their role in dental evolution
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Expressing:

Article Title: Signaling-Related Mobility Changes in Bacterial Chemotaxis Receptors Revealed by Solid-State NMR
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Transformation Assay:

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Hybridization:

Article Title: Open chromatin structures regulate the efficiencies of pre-RC formation and replication initiation in Epstein-Barr virus
Article Snippet: Whole genome amplification Co-precipitated DNA was amplified before microarray hybridization using WGA II (Sigma-Aldrich) according to the manufacturer’s instructions. .. The PCR was performed in a thermocycler (Mastercycler personal; Eppendorf) using 15 cycles.

Article Title: Mutational Signature of Aristolochic Acid Exposure as Revealed by Whole-Exome Sequencing
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Article Title: Revisiting Meiosis in Sugarcane: Chromosomal Irregularities and the Prevalence of Bivalent Configurations
Article Snippet: The hybridization mixture consisted of formamide (50%, v/v), dextran sulfate (10%, w/v), saline sodium citrate (2 × SSC), sodium dodecyl sulfate (0.13%, w/v SDS) and 3 ng/μl of probe. .. 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).

Sequencing:

Article Title: Deep-branching Novel Lineages and High Diversity of Haptophytes in the Skagerrak (Norway) Uncovered by 454 Pyrosequencing
Article Snippet: Paragraph title: RNA extraction, PCR, and sequencing ... The reaction was incubated at 25 °C for 10 min before cDNA synthesis took place at 42 °C for 75 min in a thermocycler (Mastercycler ep gradient S; Eppendorf, Hamburg, Germany).

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. .. The RFLPs enabled the selection of distinct Symbiodinium lineages for sequencing.

Nick Translation:

Article Title: Revisiting Meiosis in Sugarcane: Chromosomal Irregularities and the Prevalence of Bivalent Configurations
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other:

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Electroporation Bacterial Transformation:

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Recombinant:

Article Title: Broadcast Spawning Coral Mussismilia hispida Can Vertically Transfer its Associated Bacterial Core
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DNA Extraction:

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Nucleic Acid Electrophoresis:

Article Title: Deep-branching Novel Lineages and High Diversity of Haptophytes in the Skagerrak (Norway) Uncovered by 454 Pyrosequencing
Article Snippet: If a PCR product could be detected by gel electrophoresis, the RNA eluate was treated with additional DNase (TURBO DNase kit; Ambion, Austin, TX), according to the protocol from the manufacturer. cDNA was reverse-transcribed from RNA using High-Fidelity 1st Strand cDNA Synthesis Kit (Agilent, Santa Clara, CA) with random primers, according to the protocol from the manufacturer. .. The reaction was incubated at 25 °C for 10 min before cDNA synthesis took place at 42 °C for 75 min in a thermocycler (Mastercycler ep gradient S; Eppendorf, Hamburg, Germany).

Fluorescence:

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). .. Slides were examined under a fluorescence microscope (Olympus BX51) and images captured (Olympus DP72 camera) using DP2-BSW software (Olympus).

Magnetic Beads:

Article Title: Mutational Signature of Aristolochic Acid Exposure as Revealed by Whole-Exome Sequencing
Article Snippet: After hybridization, five steps were performed to recover and amplify captured DNA library. (i) Magnetic beads for recovering captured DNA: 50 μl of Dynal MyOne Streptavidin C1 magnetic beads (catalog no. 650.02, Invitrogen Dynal AS) was placed in a 1.5-ml microfuge tube and vigorously resuspended on a vortex mixer. .. 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.

RNA Extraction:

Article Title: Deep-branching Novel Lineages and High Diversity of Haptophytes in the Skagerrak (Norway) Uncovered by 454 Pyrosequencing
Article Snippet: Paragraph title: RNA extraction, PCR, and sequencing ... The reaction was incubated at 25 °C for 10 min before cDNA synthesis took place at 42 °C for 75 min in a thermocycler (Mastercycler ep gradient S; Eppendorf, Hamburg, Germany).

Article Title: Highly sensitive detection of the group A Rotavirus using Apolipoprotein H-coated ELISA plates compared to quantitative real-time PCR
Article Snippet: A volume of 100 μl of each sample was resuspended directly in 400 μl AVL lysis buffer (RNeasy viral RNA kit, Qiagen, Hilden, Germany) and incubated for 10 min at room temperature followed by RNA extraction according to the manufacturer's recommendations. .. The reaction was run in a thermocycler (Mastercycler epgradient, Eppendorf) for 60 min at 42°C followed by 15 min at 72°C before cooling to 4°C and storage at -20°C.

Electrophoretic Mobility Shift Assay:

Article Title: Identification of novel Fgf enhancers and their role in dental evolution
Article Snippet: Paragraph title: Electrophoretic mobility shift assay ... Control (labeled) and ECR (cold inhibitor) oligonucleotides were annealed in a thermocycler (Eppendorf) (see for list of primers).

Purification:

Article Title: Open chromatin structures regulate the efficiencies of pre-RC formation and replication initiation in Epstein-Barr virus
Article Snippet: 10 µl of the purified ChIP DNA and 100 ng of purified input DNA were used for amplification. .. The PCR was performed in a thermocycler (Mastercycler personal; Eppendorf) using 15 cycles.

Article Title: Revisiting Meiosis in Sugarcane: Chromosomal Irregularities and the Prevalence of Bivalent Configurations
Article Snippet: Purified DNAs were labeled by nick translation (Roche) with digoxigenin-11-dUTP, following the manufacturer’s instructions. .. 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).

Article Title: Identification of novel Fgf enhancers and their role in dental evolution
Article Snippet: Control (labeled) and ECR (cold inhibitor) oligonucleotides were annealed in a thermocycler (Eppendorf) (see for list of primers). .. Control oligonucleotides were labeled with [γ-32 P]rATP utilizing T4 polynucleotide kinase and purified.

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.

Polymerase Chain Reaction:

Article Title: Deep-branching Novel Lineages and High Diversity of Haptophytes in the Skagerrak (Norway) Uncovered by 454 Pyrosequencing
Article Snippet: Paragraph title: RNA extraction, PCR, and sequencing ... The reaction was incubated at 25 °C for 10 min before cDNA synthesis took place at 42 °C for 75 min in a thermocycler (Mastercycler ep gradient S; Eppendorf, Hamburg, Germany).

Article Title: Molecular detection of vanA and vanB genes among vancomycin-resistant enterococci in ICU-hospitalized patients in Ahvaz in southwest of Iran
Article Snippet: Paragraph title: The multiplex PCR method ... VanA and vanB genes were amplified using the following primers in a thermocycler (Eppendorf): A1 5′- GGGAAAACGACAATTGC-3 and A2 5-GTACAATGCGGCCGTTA-3′ with a product size of 732 bp for vanA ; B1 5′-ATGGGAAGCCGATAGTC-3′ and B2 5′-GATTTCGTTCCTCGA CC-3′ with a product size of 635 bp for vanB .

Article Title: Open chromatin structures regulate the efficiencies of pre-RC formation and replication initiation in Epstein-Barr virus
Article Snippet: .. The PCR was performed in a thermocycler (Mastercycler personal; Eppendorf) using 15 cycles. .. The amplified DNA was purified via NucleoSpin Extract II according to manufacturer’s instructions.

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: Arsenic Resistance and Prevalence of Arsenic Resistance Genes in Campylobacter jejuni and Campylobacter coli Isolated from Retail Meats
Article Snippet: DNA Extraction Bacterial DNA extracts used in polymerase chain reaction (PCR) were prepared from Campylobacter cultures using the single-cell lysing buffer (SCLB) method [ ]. .. The cells were lysed by heating at 80 °C for 10 min, followed by cooling to 55 °C for 10 min, using a thermocycler (Eppendorf, Hamburg, Germany).

Article Title: Mutational Signature of Aristolochic Acid Exposure as Revealed by Whole-Exome Sequencing
Article Snippet: Human exome capture was performed following a protocol from Agilent’s SureSelectXT Human All Exon V4 (catalog no. 5190-4634, Agilent) with the following modifications. (i) A hybridization mixture was prepared containing 25 μl of SureSelect Hyb #1, 1 μl of SureSelect Hyb #2, 10 μl of SureSelect Hyb #3, and 13 μl of SureSelect Hyb #4. (ii) PE-library DNA (3.4 μl, 0.5 μg) described above, SureSelect Block #1 (2.5 μl), SureSelect Block #2 (2.5 μl), and Block #3 (0.6 μl) were loaded into one well in a 384-well Diamond PCR plate (catalog no. AB-1111, Thermo Scientific), sealed with MicroAmp clear adhesive film (catalog no. 4306311; ABI), placed in GeneAmp PCR System 9700 thermocycler (Life Sciences Inc.) for 5 min at 95°C, and then held at 65°C (with the heated lid on). (iii) Hybridization buffer (25 to 30 μl) from step (i) was heated for at least 5 min at 65°C in another sealed plate with heated lid on. (iv) SureSelect Oligo Capture Library (5 μl), nuclease-free water (1 μl), and diluted RNase Block (1 μl) (prepared by diluting RNase Block 1:1 with nuclease-free water) were mixed and heated at 65°C for 2 min in another sealed 384-well plate. (v) While keeping all reactions at 65°C, 13 μl of hybridization buffer from step (iii) was added to the 7 μl of the SureSelect Capture Library Mix from step (iv) and then the entire contents (9 μl) of the library from step (ii). .. 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: Our probes consisted of CENT repeats obtained by amplification of genomic DNA from “Caiana Fita” and IACSP93-3046, and the PCR product was purified as detailed above. .. 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).

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.

Selection:

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. .. The RFLPs enabled the selection of distinct Symbiodinium lineages for sequencing.

Labeling:

Article Title: Revisiting Meiosis in Sugarcane: Chromosomal Irregularities and the Prevalence of Bivalent Configurations
Article Snippet: Purified DNAs were labeled by nick translation (Roche) with digoxigenin-11-dUTP, following the manufacturer’s instructions. .. 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).

Article Title: Identification of novel Fgf enhancers and their role in dental evolution
Article Snippet: .. Control (labeled) and ECR (cold inhibitor) oligonucleotides were annealed in a thermocycler (Eppendorf) (see for list of primers). .. Control oligonucleotides were labeled with [γ-32 P]rATP utilizing T4 polynucleotide kinase and purified.

Lysis:

Article Title: Highly sensitive detection of the group A Rotavirus using Apolipoprotein H-coated ELISA plates compared to quantitative real-time PCR
Article Snippet: A volume of 100 μl of each sample was resuspended directly in 400 μl AVL lysis buffer (RNeasy viral RNA kit, Qiagen, Hilden, Germany) and incubated for 10 min at room temperature followed by RNA extraction according to the manufacturer's recommendations. .. The reaction was run in a thermocycler (Mastercycler epgradient, Eppendorf) for 60 min at 42°C followed by 15 min at 72°C before cooling to 4°C and storage at -20°C.

Chloramphenicol Acetyltransferase Assay:

Article Title: Highly sensitive detection of the group A Rotavirus using Apolipoprotein H-coated ELISA plates compared to quantitative real-time PCR
Article Snippet: The reaction was run in a thermocycler (Mastercycler epgradient, Eppendorf) for 60 min at 42°C followed by 15 min at 72°C before cooling to 4°C and storage at -20°C. .. The GE of rotavirus were determined by a qPCR assay, using 5' nuclease probes (TaqMan® probes) with primer combination RoA_25/26 and probe TM3 (RoA_TM3 probe YAK-CTT ITC CAT CTT TCC gCA CgC gCT--DB, TIB Molbiol), which was designed to detect all human and animal RV-A by binding within a conserved region of the NSP4 gene.

Chromatin Immunoprecipitation:

Article Title: Open chromatin structures regulate the efficiencies of pre-RC formation and replication initiation in Epstein-Barr virus
Article Snippet: 10 µl of the purified ChIP DNA and 100 ng of purified input DNA were used for amplification. .. The PCR was performed in a thermocycler (Mastercycler personal; Eppendorf) using 15 cycles.

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).

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). .. Preparations were counterstained and mounted with DAPI in VECTASHIELD medium (Vector).

Article Title: Signaling-Related Mobility Changes in Bacterial Chemotaxis Receptors Revealed by Solid-State NMR
Article Snippet: Paragraph title: Plasmid Construction ... The PCR reactions were done in a thermocycler (Eppendorf Master Cycler personal or BioRad MJ Mini) using reagents from New England Biolabs.

Software:

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). .. Slides were examined under a fluorescence microscope (Olympus BX51) and images captured (Olympus DP72 camera) using DP2-BSW software (Olympus).

Microscopy:

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). .. Slides were examined under a fluorescence microscope (Olympus BX51) and images captured (Olympus DP72 camera) using DP2-BSW software (Olympus).

Multiplex Assay:

Article Title: Molecular detection of vanA and vanB genes among vancomycin-resistant enterococci in ICU-hospitalized patients in Ahvaz in southwest of Iran
Article Snippet: Paragraph title: The multiplex PCR method ... VanA and vanB genes were amplified using the following primers in a thermocycler (Eppendorf): A1 5′- GGGAAAACGACAATTGC-3 and A2 5-GTACAATGCGGCCGTTA-3′ with a product size of 732 bp for vanA ; B1 5′-ATGGGAAGCCGATAGTC-3′ and B2 5′-GATTTCGTTCCTCGA CC-3′ with a product size of 635 bp for vanB .

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. ..

Article Title: Highly sensitive detection of the group A Rotavirus using Apolipoprotein H-coated ELISA plates compared to quantitative real-time PCR
Article Snippet: The reaction was run in a thermocycler (Mastercycler epgradient, Eppendorf) for 60 min at 42°C followed by 15 min at 72°C before cooling to 4°C and storage at -20°C. .. The GE of rotavirus were determined by a qPCR assay, using 5' nuclease probes (TaqMan® probes) with primer combination RoA_25/26 and probe TM3 (RoA_TM3 probe YAK-CTT ITC CAT CTT TCC gCA CgC gCT--DB, TIB Molbiol), which was designed to detect all human and animal RV-A by binding within a conserved region of the NSP4 gene.

Size-exclusion Chromatography:

Article Title: Highly sensitive detection of the group A Rotavirus using Apolipoprotein H-coated ELISA plates compared to quantitative real-time PCR
Article Snippet: RNA was incubated with 2 μl primer mix of random hexamers (R6)/specific RoA_25/26 primers (RoA_25 gCT TTT AAA AgT TCT gTT CCg Ag; RoA_26 CTC AAT gTg TAR TTg Agg TCg, TIB Molbiol, Berlin, Germany) for 30 sec at 93°C. .. The reaction was run in a thermocycler (Mastercycler epgradient, Eppendorf) for 60 min at 42°C followed by 15 min at 72°C before cooling to 4°C and storage at -20°C.

Concentration Assay:

Article Title: Molecular detection of vanA and vanB genes among vancomycin-resistant enterococci in ICU-hospitalized patients in Ahvaz in southwest of Iran
Article Snippet: DNA extraction from Enterococcus isolates was carried out by the boiling method, and DNA concentration was measured by biophotometer (Eppendorf, Hamburg, Germany). .. VanA and vanB genes were amplified using the following primers in a thermocycler (Eppendorf): A1 5′- GGGAAAACGACAATTGC-3 and A2 5-GTACAATGCGGCCGTTA-3′ with a product size of 732 bp for vanA ; B1 5′-ATGGGAAGCCGATAGTC-3′ and B2 5′-GATTTCGTTCCTCGA CC-3′ with a product size of 635 bp for vanB .

Construct:

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.

Lamp Assay:

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

Gel Extraction:

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. .. PCR products were separated in 1% Agarose gels, and each product with the expected length was gel-purified (QiAquick gel extraction Kit, Qiagen).

Fluorescence In Situ Hybridization:

Article Title: Revisiting Meiosis in Sugarcane: Chromosomal Irregularities and the Prevalence of Bivalent Configurations
Article Snippet: Paragraph title: Chromosome Association Analysis Using FISH ... 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).

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  • 92
    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: 92/100, based on 14 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/conventional thermocycler/product/Eppendorf AG
    Average 92 stars, based on 14 article reviews
    Price from $9.99 to $1999.99
    conventional thermocycler - by Bioz Stars, 2020-04
    92/100 stars
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    86
    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: 86/100, 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 86 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    thermocycler 2 - by Bioz Stars, 2020-04
    86/100 stars
      Buy from Supplier

    86
    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: 86/100, 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 86 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    thermocycler 1 - by Bioz Stars, 2020-04
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      Buy from Supplier

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    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