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Bio-Rad polymerase chain reaction fragments
Polymerase Chain Reaction Fragments, supplied by Bio-Rad, used in various techniques. Bioz Stars score: 88/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Electroporation:

Article Title: Phage-Based Fluorescent Biosensor Prototypes to Specifically Detect Enteric Bacteria Such as E. coli and Salmonella enterica Typhimurium
Article Snippet: .. After a purification step using the MinElute reaction cleanup kit (Qiagen), 1.5 μg of PCR fragments were electroporated into LCB6205(HK620)/pKD46 and LT2(P22)/pKD46 using the Gene PulserXcell electroporation system (Biorad). .. Fluorescent colonies were selected with a Fujifilm FLA-5100 scanner.

Centrifugation:

Article Title: Comprehensive Mutational Analysis of the Moloney Murine Leukemia Virus Envelope Protein
Article Snippet: .. The supernatant containing the released radiolabeled PCR fragments was separated from the beads by centrifugation through a Micro Bio-Spin column (Bio-Rad) and then concentrated by ethanol precipitation. .. Samples were analyzed by denaturing polyacrylamide gel electrophoresis, and the fragments representing the mutants were visualized with a Molecular Dynamics PhosphorImager.

Ethanol Precipitation:

Article Title: Comprehensive Mutational Analysis of the Moloney Murine Leukemia Virus Envelope Protein
Article Snippet: .. The supernatant containing the released radiolabeled PCR fragments was separated from the beads by centrifugation through a Micro Bio-Spin column (Bio-Rad) and then concentrated by ethanol precipitation. .. Samples were analyzed by denaturing polyacrylamide gel electrophoresis, and the fragments representing the mutants were visualized with a Molecular Dynamics PhosphorImager.

Purification:

Article Title: Phage-Based Fluorescent Biosensor Prototypes to Specifically Detect Enteric Bacteria Such as E. coli and Salmonella enterica Typhimurium
Article Snippet: .. After a purification step using the MinElute reaction cleanup kit (Qiagen), 1.5 μg of PCR fragments were electroporated into LCB6205(HK620)/pKD46 and LT2(P22)/pKD46 using the Gene PulserXcell electroporation system (Biorad). .. Fluorescent colonies were selected with a Fujifilm FLA-5100 scanner.

Article Title: Characterization of the Cryptic AV3 Promoter of Ageratum Yellow Vein Virus in Prokaryotic and Eukaryotic Systems
Article Snippet: .. For South-western blot, the PCR fragments in agarose gels were transferred to nitrocellulose (NC) membranes and incubated with 100 µg purified His6 -tagged SSB proteins at RT for 1 h. The bound SSB proteins on the PCR fragments on NC membranes were detected by a monoclonal antibody against histidine tag (AbD Serotec, Kidlington, Oxford, UK), and followed a rabbit anti-mouse IgG AP-conjugated antibody. .. Co-expression of AYVV-NT-encoded proteins with AV3 and rrn B P1 promoter Each of the plasmids pBT-1634SacI, pBT-AV1, pBT-CP, pBT-Rep, pBT-TrAP, pBT-Ren, and pBT-C4 was co-transformed with the pAY-WT or prrn B-P1 , in which the rrn B P1 promoter was cloned into the GFP-reporter vector pGlow-TOPO, into the E. coli XLI-BLUE MRF' strain.

Electrophoresis:

Article Title: Anti-inflammatory and Intestinal Barrier-protective Activities of Commensal Lactobacilli and Bifidobacteria in Thoroughbreds: Role of Probiotics in Diarrhea Prevention in Neonatal Thoroughbreds
Article Snippet: .. The PCR fragments were separated by DGGE using the DCode system (Bio-Rad Laboratories, Hercules, USA) with the following modifications: For the DGGE analysis of bacteria, 8% (wt/vol) polyacrylamide gels were prepared using a denaturing gradient ranging from 35 to 50%, and electrophoresis was performed in Tris-acetate-EDTA (TAE) buffer for 14 hr at a constant voltage of 60 V. A 100% denaturant corresponded to 7 M urea and 40% formamide. .. After electrophoresis, the gels were stained for 15 min using an ethidium bromide solution (250 ml TAE buffer + 25 µl of 10 mg/ml ethidium bromide solution).

Incubation:

Article Title: Characterization of the Cryptic AV3 Promoter of Ageratum Yellow Vein Virus in Prokaryotic and Eukaryotic Systems
Article Snippet: .. For South-western blot, the PCR fragments in agarose gels were transferred to nitrocellulose (NC) membranes and incubated with 100 µg purified His6 -tagged SSB proteins at RT for 1 h. The bound SSB proteins on the PCR fragments on NC membranes were detected by a monoclonal antibody against histidine tag (AbD Serotec, Kidlington, Oxford, UK), and followed a rabbit anti-mouse IgG AP-conjugated antibody. .. Co-expression of AYVV-NT-encoded proteins with AV3 and rrn B P1 promoter Each of the plasmids pBT-1634SacI, pBT-AV1, pBT-CP, pBT-Rep, pBT-TrAP, pBT-Ren, and pBT-C4 was co-transformed with the pAY-WT or prrn B-P1 , in which the rrn B P1 promoter was cloned into the GFP-reporter vector pGlow-TOPO, into the E. coli XLI-BLUE MRF' strain.

Southwestern Blot:

Article Title: Characterization of the Cryptic AV3 Promoter of Ageratum Yellow Vein Virus in Prokaryotic and Eukaryotic Systems
Article Snippet: .. For South-western blot, the PCR fragments in agarose gels were transferred to nitrocellulose (NC) membranes and incubated with 100 µg purified His6 -tagged SSB proteins at RT for 1 h. The bound SSB proteins on the PCR fragments on NC membranes were detected by a monoclonal antibody against histidine tag (AbD Serotec, Kidlington, Oxford, UK), and followed a rabbit anti-mouse IgG AP-conjugated antibody. .. Co-expression of AYVV-NT-encoded proteins with AV3 and rrn B P1 promoter Each of the plasmids pBT-1634SacI, pBT-AV1, pBT-CP, pBT-Rep, pBT-TrAP, pBT-Ren, and pBT-C4 was co-transformed with the pAY-WT or prrn B-P1 , in which the rrn B P1 promoter was cloned into the GFP-reporter vector pGlow-TOPO, into the E. coli XLI-BLUE MRF' strain.

Polymerase Chain Reaction:

Article Title: Anti-inflammatory and Intestinal Barrier-protective Activities of Commensal Lactobacilli and Bifidobacteria in Thoroughbreds: Role of Probiotics in Diarrhea Prevention in Neonatal Thoroughbreds
Article Snippet: .. The PCR fragments were separated by DGGE using the DCode system (Bio-Rad Laboratories, Hercules, USA) with the following modifications: For the DGGE analysis of bacteria, 8% (wt/vol) polyacrylamide gels were prepared using a denaturing gradient ranging from 35 to 50%, and electrophoresis was performed in Tris-acetate-EDTA (TAE) buffer for 14 hr at a constant voltage of 60 V. A 100% denaturant corresponded to 7 M urea and 40% formamide. .. After electrophoresis, the gels were stained for 15 min using an ethidium bromide solution (250 ml TAE buffer + 25 µl of 10 mg/ml ethidium bromide solution).

Article Title: Phage-Based Fluorescent Biosensor Prototypes to Specifically Detect Enteric Bacteria Such as E. coli and Salmonella enterica Typhimurium
Article Snippet: .. After a purification step using the MinElute reaction cleanup kit (Qiagen), 1.5 μg of PCR fragments were electroporated into LCB6205(HK620)/pKD46 and LT2(P22)/pKD46 using the Gene PulserXcell electroporation system (Biorad). .. Fluorescent colonies were selected with a Fujifilm FLA-5100 scanner.

Article Title: Development of a Potential Probiotic Fresh Cheese Using Two Lactobacillus salivarius Strains Isolated from Human Milk
Article Snippet: .. PCR fragments were separated by denaturing gradient gel electrophoresis (DGGE) using a DCode System (BioRad Laboratories, Inc., Hercules, California, USA) and gels with a linear denaturant gradient of 30 to 50% as described by Martín et al. [ ]. .. A DNA mixture made with equal amounts of amplicons from L. salivarius CECT5713 or PS2 and Lc. lactis ESI153 was used as a marker.

Article Title: Molecular Monitoring of Succession of Bacterial Communities in Human Neonates
Article Snippet: .. PCR fragments, also called amplicons, were separated by DGGE by using the specifications of Muyzer et al. ( ) and the Decode system (Bio-Rad Laboratories, Hercules, Calif.), with the following modifications. ..

Article Title: Characterization of the Cryptic AV3 Promoter of Ageratum Yellow Vein Virus in Prokaryotic and Eukaryotic Systems
Article Snippet: .. For South-western blot, the PCR fragments in agarose gels were transferred to nitrocellulose (NC) membranes and incubated with 100 µg purified His6 -tagged SSB proteins at RT for 1 h. The bound SSB proteins on the PCR fragments on NC membranes were detected by a monoclonal antibody against histidine tag (AbD Serotec, Kidlington, Oxford, UK), and followed a rabbit anti-mouse IgG AP-conjugated antibody. .. Co-expression of AYVV-NT-encoded proteins with AV3 and rrn B P1 promoter Each of the plasmids pBT-1634SacI, pBT-AV1, pBT-CP, pBT-Rep, pBT-TrAP, pBT-Ren, and pBT-C4 was co-transformed with the pAY-WT or prrn B-P1 , in which the rrn B P1 promoter was cloned into the GFP-reporter vector pGlow-TOPO, into the E. coli XLI-BLUE MRF' strain.

Article Title: Comprehensive Mutational Analysis of the Moloney Murine Leukemia Virus Envelope Protein
Article Snippet: .. The supernatant containing the released radiolabeled PCR fragments was separated from the beads by centrifugation through a Micro Bio-Spin column (Bio-Rad) and then concentrated by ethanol precipitation. .. Samples were analyzed by denaturing polyacrylamide gel electrophoresis, and the fragments representing the mutants were visualized with a Molecular Dynamics PhosphorImager.

Article Title: Optimising Bacterial DNA Extraction from Faecal Samples: Comparison of Three Methods
Article Snippet: .. DGGE of PCR Amplicons The PCR fragments were separated by DGGE as described by Myuzer [ ] with the DCode System as manufacturer prescribes (Bio-Rad Laboratories, Hercules, USA), 8% Polyacrylamide (vol/vol) (ratio of acrylamide:bisacrylamide [37.5:1]) in 0.5×TAE buffer; (pH 8.0) and using a gradient ranging from 30% to 65% denaturant (100% denaturant acrylamide corresponds to 7 M urea and 40% (vol/vol) formamide). ..

Denaturing Gradient Gel Electrophoresis:

Article Title: Anti-inflammatory and Intestinal Barrier-protective Activities of Commensal Lactobacilli and Bifidobacteria in Thoroughbreds: Role of Probiotics in Diarrhea Prevention in Neonatal Thoroughbreds
Article Snippet: .. The PCR fragments were separated by DGGE using the DCode system (Bio-Rad Laboratories, Hercules, USA) with the following modifications: For the DGGE analysis of bacteria, 8% (wt/vol) polyacrylamide gels were prepared using a denaturing gradient ranging from 35 to 50%, and electrophoresis was performed in Tris-acetate-EDTA (TAE) buffer for 14 hr at a constant voltage of 60 V. A 100% denaturant corresponded to 7 M urea and 40% formamide. .. After electrophoresis, the gels were stained for 15 min using an ethidium bromide solution (250 ml TAE buffer + 25 µl of 10 mg/ml ethidium bromide solution).

Article Title: Development of a Potential Probiotic Fresh Cheese Using Two Lactobacillus salivarius Strains Isolated from Human Milk
Article Snippet: .. PCR fragments were separated by denaturing gradient gel electrophoresis (DGGE) using a DCode System (BioRad Laboratories, Inc., Hercules, California, USA) and gels with a linear denaturant gradient of 30 to 50% as described by Martín et al. [ ]. .. A DNA mixture made with equal amounts of amplicons from L. salivarius CECT5713 or PS2 and Lc. lactis ESI153 was used as a marker.

Article Title: Molecular Monitoring of Succession of Bacterial Communities in Human Neonates
Article Snippet: .. PCR fragments, also called amplicons, were separated by DGGE by using the specifications of Muyzer et al. ( ) and the Decode system (Bio-Rad Laboratories, Hercules, Calif.), with the following modifications. ..

Article Title: Optimising Bacterial DNA Extraction from Faecal Samples: Comparison of Three Methods
Article Snippet: .. DGGE of PCR Amplicons The PCR fragments were separated by DGGE as described by Myuzer [ ] with the DCode System as manufacturer prescribes (Bio-Rad Laboratories, Hercules, USA), 8% Polyacrylamide (vol/vol) (ratio of acrylamide:bisacrylamide [37.5:1]) in 0.5×TAE buffer; (pH 8.0) and using a gradient ranging from 30% to 65% denaturant (100% denaturant acrylamide corresponds to 7 M urea and 40% (vol/vol) formamide). ..

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    Bio-Rad cdna fragment levels
    Comparison different PCR methods and impact on quantification. Graphic representation of the quantification of dystrophin <t>cDNA</t> construct templates lacking or containing exon 51 mixed in different ratios ranging from 0% to 100% using nested PCR (40, 50 and 60 cycles), <t>qPCR</t> (LinRegPCR and Pfaffl methods) and ddPCR. The dashed red line indicates the theoretical template ratios. The solid black ddPCR line is almost indistinguishable from the theoretical line and both lines are superimposed. Data is based on one experiment using 2 replicates for ddPCR and 3 replicates for qPCR.
    Cdna Fragment Levels, supplied by Bio-Rad, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Bio-Rad dna pre fragmentation
    Specificity of the three Droplet Digital PCR <t>(ddPCR)</t> systems used (A) Determination of false-positive cases (mutated MT) detected using the three ddPCR systems described in Figure 3 and a commercial genomic wild-type <t>DNA</t> control provided in the Quantifiler Human DNA Kit (Applied Biosystems, PN4344790F, Foster City, CA, USA). The commercial WT DNA was diluted and tested for L858R substitutions (Ai) , various delEX19 deletions (Aii) and T790M substitutions (Aiii) using three detection assays: Seki's assay, an in house's system and LT's system (see Table 2 ); n indicates the number of independent experiments carried out for each conditions. WT and MT colums indicate the mean of absolute detected copies. The numbers and rates of false-positives (% FP) cases are reported. (B) Background of false-positive copies (%MT) for all of the ddPCR mutation systems used to detect L858R substitutions (Bi) , various delEX19 deletions (Bii) and T790M substitutions (Biii) from cfDNA of NSCLC patients with a negative or unknown biopsy status at diagnosis and with negative results in ddPCR. The absolute copy number was based on the maximum number of MT copies observed in tables Ai-Aiii (5 MT copies) over the minimum WT detection threshold (500 WT copies).
    Dna Pre Fragmentation, supplied by Bio-Rad, used in various techniques. Bioz Stars score: 91/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Bio-Rad pcr fragments
    (A) <t>PCR-DGGE</t> profiles representing the bacterial diversity in baby L generated from samples taken from birth to 372 days. Both the day and the approximate time of the month of sampling are indicated. Changes in the diet, such as addition of formula milk, are indicated by arrows. The bands identified from the 16S rDNA clone libraries are numbered and are indicated by arrowheads; these bands are described in the table in panel B. (B) Closest relative as determined by comparative sequence analysis, level of identity with this relative, clone designation, and accession number for each band identified in panel A.
    Pcr Fragments, supplied by Bio-Rad, used in various techniques. Bioz Stars score: 94/100, based on 92 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Bio-Rad p1ap p1 bp pcr fragment
    A. <t>PCR</t> screening, using primers P1D and P1test, of plaques obtained upon phage recombineering. Lanes 4 and 11 contain PCR products that indicate the presence of P1virΔIS within the plaques. B. PCR verification of the shortening of the IS‐deleted region in a pure P1virΔIS lysate using primers P1D and P1 BP. M: 1 kb DNA ladder (Fermentas).
    P1ap P1 Bp Pcr Fragment, supplied by Bio-Rad, used in various techniques. Bioz Stars score: 85/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    Comparison different PCR methods and impact on quantification. Graphic representation of the quantification of dystrophin cDNA construct templates lacking or containing exon 51 mixed in different ratios ranging from 0% to 100% using nested PCR (40, 50 and 60 cycles), qPCR (LinRegPCR and Pfaffl methods) and ddPCR. The dashed red line indicates the theoretical template ratios. The solid black ddPCR line is almost indistinguishable from the theoretical line and both lines are superimposed. Data is based on one experiment using 2 replicates for ddPCR and 3 replicates for qPCR.

    Journal: PLoS ONE

    Article Title: Digital Droplet PCR for the Absolute Quantification of Exon Skipping Induced by Antisense Oligonucleotides in (Pre-)Clinical Development for Duchenne Muscular Dystrophy

    doi: 10.1371/journal.pone.0162467

    Figure Lengend Snippet: Comparison different PCR methods and impact on quantification. Graphic representation of the quantification of dystrophin cDNA construct templates lacking or containing exon 51 mixed in different ratios ranging from 0% to 100% using nested PCR (40, 50 and 60 cycles), qPCR (LinRegPCR and Pfaffl methods) and ddPCR. The dashed red line indicates the theoretical template ratios. The solid black ddPCR line is almost indistinguishable from the theoretical line and both lines are superimposed. Data is based on one experiment using 2 replicates for ddPCR and 3 replicates for qPCR.

    Article Snippet: In each qPCR run, a no template control (NTC) was included as negative control. cDNA fragment levels were determined on a CFX96 real-time thermal cycler (BioRad) using the following protocol: 95°C for 10 min, then 40 cycles of 95°C for 15 sec and 60°C for 1 min. qPCR data was analyzed using both the Pfaffl method [ ] and the LinRegPCR method [ ].

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

    Specificity of the three Droplet Digital PCR (ddPCR) systems used (A) Determination of false-positive cases (mutated MT) detected using the three ddPCR systems described in Figure 3 and a commercial genomic wild-type DNA control provided in the Quantifiler Human DNA Kit (Applied Biosystems, PN4344790F, Foster City, CA, USA). The commercial WT DNA was diluted and tested for L858R substitutions (Ai) , various delEX19 deletions (Aii) and T790M substitutions (Aiii) using three detection assays: Seki's assay, an in house's system and LT's system (see Table 2 ); n indicates the number of independent experiments carried out for each conditions. WT and MT colums indicate the mean of absolute detected copies. The numbers and rates of false-positives (% FP) cases are reported. (B) Background of false-positive copies (%MT) for all of the ddPCR mutation systems used to detect L858R substitutions (Bi) , various delEX19 deletions (Bii) and T790M substitutions (Biii) from cfDNA of NSCLC patients with a negative or unknown biopsy status at diagnosis and with negative results in ddPCR. The absolute copy number was based on the maximum number of MT copies observed in tables Ai-Aiii (5 MT copies) over the minimum WT detection threshold (500 WT copies).

    Journal: Oncotarget

    Article Title: Evaluation of pre-analytical conditions and comparison of the performance of several digital PCR assays for the detection of major EGFR mutations in circulating DNA from non-small cell lung cancers: the CIRCAN_0 study

    doi: 10.18632/oncotarget.21256

    Figure Lengend Snippet: Specificity of the three Droplet Digital PCR (ddPCR) systems used (A) Determination of false-positive cases (mutated MT) detected using the three ddPCR systems described in Figure 3 and a commercial genomic wild-type DNA control provided in the Quantifiler Human DNA Kit (Applied Biosystems, PN4344790F, Foster City, CA, USA). The commercial WT DNA was diluted and tested for L858R substitutions (Ai) , various delEX19 deletions (Aii) and T790M substitutions (Aiii) using three detection assays: Seki's assay, an in house's system and LT's system (see Table 2 ); n indicates the number of independent experiments carried out for each conditions. WT and MT colums indicate the mean of absolute detected copies. The numbers and rates of false-positives (% FP) cases are reported. (B) Background of false-positive copies (%MT) for all of the ddPCR mutation systems used to detect L858R substitutions (Bi) , various delEX19 deletions (Bii) and T790M substitutions (Biii) from cfDNA of NSCLC patients with a negative or unknown biopsy status at diagnosis and with negative results in ddPCR. The absolute copy number was based on the maximum number of MT copies observed in tables Ai-Aiii (5 MT copies) over the minimum WT detection threshold (500 WT copies).

    Article Snippet: Consequently, all samples could be directly analyzed by ddPCR without DNA pre-fragmentation, which is highly recommended by Bio-Rad for the amplification of genomic DNA.

    Techniques: Digital PCR, Mutagenesis

    Impact of pre-analytical blood storage conditions in EDTA tubes on circulating free DNA (cfDNA) integrity (A) Evaluation of the effect of blood storage time (4 hours or 24 hours) and temperature (room temperature RT or 4°C) in EDTA tubes prior to plasma collection, on the concentration (ng/μL) of cfDNA extracted using the Qubit Quantification Kit (Ai) , and the number of amplifiable DNA copies using the Quantifiler technique (Aii) . Blood samples from the same patient (n = 7) were processed according to the three storage conditions. (B) Exploration of the number of wild-type (WT) copies of 3 independent regions of EGFR gene with the different ddPCR systems detailed in Figure 3 for WT L858R (Bi) , WT delEX19 (Bii) and WT T790M (Biii) when samples are processed within 4 hours and within 24 hours after blood sampling (data not paired).

    Journal: Oncotarget

    Article Title: Evaluation of pre-analytical conditions and comparison of the performance of several digital PCR assays for the detection of major EGFR mutations in circulating DNA from non-small cell lung cancers: the CIRCAN_0 study

    doi: 10.18632/oncotarget.21256

    Figure Lengend Snippet: Impact of pre-analytical blood storage conditions in EDTA tubes on circulating free DNA (cfDNA) integrity (A) Evaluation of the effect of blood storage time (4 hours or 24 hours) and temperature (room temperature RT or 4°C) in EDTA tubes prior to plasma collection, on the concentration (ng/μL) of cfDNA extracted using the Qubit Quantification Kit (Ai) , and the number of amplifiable DNA copies using the Quantifiler technique (Aii) . Blood samples from the same patient (n = 7) were processed according to the three storage conditions. (B) Exploration of the number of wild-type (WT) copies of 3 independent regions of EGFR gene with the different ddPCR systems detailed in Figure 3 for WT L858R (Bi) , WT delEX19 (Bii) and WT T790M (Biii) when samples are processed within 4 hours and within 24 hours after blood sampling (data not paired).

    Article Snippet: Consequently, all samples could be directly analyzed by ddPCR without DNA pre-fragmentation, which is highly recommended by Bio-Rad for the amplification of genomic DNA.

    Techniques: Concentration Assay, Sampling

    Accuracy of the three Droplet Digital PCR (ddPCR) systems used (A) Top, correlation between the theoretical expected number of wild-type (WT) copies and experimentally measured WT copies of commercial genomic DNA from the Quantifiler Human DNA Quantification Kit (Applied Biosystems, PN4344790F, Foster City, CA, USA) by ddPCR for the detection of (Ai) L858R substitutions, (Aii) delEX19 deletions and (Aiii) T790M substitutions, according to the detection assay used, namely Seki's assay, Life Technologies' (LT's) assay, or our in-house assay. Bottom, tables summarizing statistical data presented above. (B) Top, correlation between the number of WT copies for (Bi) L858R substitutions, (Bii) delEX19 deletions and (Biii) substitutions T790M and the concentration of cfDNA (in ng/μL) measured by Qubit (Life Technologies, Q32854, Carlsbad, CA, USA) in cfDNA samples. Bottom, equation used to estimate the concentration of cfDNA required to detect a threshold level of 1,000 mutated copies, for each plot presented above.

    Journal: Oncotarget

    Article Title: Evaluation of pre-analytical conditions and comparison of the performance of several digital PCR assays for the detection of major EGFR mutations in circulating DNA from non-small cell lung cancers: the CIRCAN_0 study

    doi: 10.18632/oncotarget.21256

    Figure Lengend Snippet: Accuracy of the three Droplet Digital PCR (ddPCR) systems used (A) Top, correlation between the theoretical expected number of wild-type (WT) copies and experimentally measured WT copies of commercial genomic DNA from the Quantifiler Human DNA Quantification Kit (Applied Biosystems, PN4344790F, Foster City, CA, USA) by ddPCR for the detection of (Ai) L858R substitutions, (Aii) delEX19 deletions and (Aiii) T790M substitutions, according to the detection assay used, namely Seki's assay, Life Technologies' (LT's) assay, or our in-house assay. Bottom, tables summarizing statistical data presented above. (B) Top, correlation between the number of WT copies for (Bi) L858R substitutions, (Bii) delEX19 deletions and (Biii) substitutions T790M and the concentration of cfDNA (in ng/μL) measured by Qubit (Life Technologies, Q32854, Carlsbad, CA, USA) in cfDNA samples. Bottom, equation used to estimate the concentration of cfDNA required to detect a threshold level of 1,000 mutated copies, for each plot presented above.

    Article Snippet: Consequently, all samples could be directly analyzed by ddPCR without DNA pre-fragmentation, which is highly recommended by Bio-Rad for the amplification of genomic DNA.

    Techniques: Digital PCR, Detection Assay, Concentration Assay

    Sensitivity of the three Droplet Digital PCR (ddPCR) systems used Correlation between measured mutated (MT) and wild-type (WT) copies with the theoretical percentage of mutated copies of four reference standards DNA (Horizon Diagnostics) for three somatic EGFR alterations L858R and T790M substitutions, and various delEX19 deletions detected using the ddPCR systems described in Figure 3 and Table 2 . The commercial standard DNA was tested for (Ai) L858R mutations with Seki's, Life Technologies' (LT's) and our in-house primers/probes. (Aii) delEX19 deletions were detected using the same three systems, while (Aiii) T790M mutations were detected using Seki's and LT's primers/probes. (B) Representation of the size of the amplicons generated during ddPCR with Seki's primer and our in-house primers for the L858R (Bi) and delEX19 (Bii) gene regions. n indicates the number of independent experiments carried out for each conditions. WT and MT colums indicate the mean of absolute detected copies. (C) Histogram presenting the number of WT copies detected using Seki's and LT's primers/probes for L858R mutations (Ci) and delEX19 deletions (Cii) . The ratio represents the difference in the number of MT copies detected between our in-house primers and Seki's primers.

    Journal: Oncotarget

    Article Title: Evaluation of pre-analytical conditions and comparison of the performance of several digital PCR assays for the detection of major EGFR mutations in circulating DNA from non-small cell lung cancers: the CIRCAN_0 study

    doi: 10.18632/oncotarget.21256

    Figure Lengend Snippet: Sensitivity of the three Droplet Digital PCR (ddPCR) systems used Correlation between measured mutated (MT) and wild-type (WT) copies with the theoretical percentage of mutated copies of four reference standards DNA (Horizon Diagnostics) for three somatic EGFR alterations L858R and T790M substitutions, and various delEX19 deletions detected using the ddPCR systems described in Figure 3 and Table 2 . The commercial standard DNA was tested for (Ai) L858R mutations with Seki's, Life Technologies' (LT's) and our in-house primers/probes. (Aii) delEX19 deletions were detected using the same three systems, while (Aiii) T790M mutations were detected using Seki's and LT's primers/probes. (B) Representation of the size of the amplicons generated during ddPCR with Seki's primer and our in-house primers for the L858R (Bi) and delEX19 (Bii) gene regions. n indicates the number of independent experiments carried out for each conditions. WT and MT colums indicate the mean of absolute detected copies. (C) Histogram presenting the number of WT copies detected using Seki's and LT's primers/probes for L858R mutations (Ci) and delEX19 deletions (Cii) . The ratio represents the difference in the number of MT copies detected between our in-house primers and Seki's primers.

    Article Snippet: Consequently, all samples could be directly analyzed by ddPCR without DNA pre-fragmentation, which is highly recommended by Bio-Rad for the amplification of genomic DNA.

    Techniques: Digital PCR, Generated

    (A) PCR-DGGE profiles representing the bacterial diversity in baby L generated from samples taken from birth to 372 days. Both the day and the approximate time of the month of sampling are indicated. Changes in the diet, such as addition of formula milk, are indicated by arrows. The bands identified from the 16S rDNA clone libraries are numbered and are indicated by arrowheads; these bands are described in the table in panel B. (B) Closest relative as determined by comparative sequence analysis, level of identity with this relative, clone designation, and accession number for each band identified in panel A.

    Journal: Applied and Environmental Microbiology

    Article Title: Molecular Monitoring of Succession of Bacterial Communities in Human Neonates

    doi: 10.1128/AEM.68.1.219-226.2002

    Figure Lengend Snippet: (A) PCR-DGGE profiles representing the bacterial diversity in baby L generated from samples taken from birth to 372 days. Both the day and the approximate time of the month of sampling are indicated. Changes in the diet, such as addition of formula milk, are indicated by arrows. The bands identified from the 16S rDNA clone libraries are numbered and are indicated by arrowheads; these bands are described in the table in panel B. (B) Closest relative as determined by comparative sequence analysis, level of identity with this relative, clone designation, and accession number for each band identified in panel A.

    Article Snippet: PCR fragments, also called amplicons, were separated by DGGE by using the specifications of Muyzer et al. ( ) and the Decode system (Bio-Rad Laboratories, Hercules, Calif.), with the following modifications.

    Techniques: Polymerase Chain Reaction, Denaturing Gradient Gel Electrophoresis, Generated, Sampling, Sequencing

    (A) PCR-DGGE profiles representing the bacterial diversity in baby D generated from samples taken from birth to 323 days. Both the day and the approximate time of the month of sampling are indicated. Changes in the diet are indicated by arrows. The bands identified from the 16S rDNA clone libraries are numbered and are indicated by arrowheads; these bands are described in the table in panel B. (B) Closest relative as determined by comparative sequence analysis, level of identity with this relative, clone designation, and accession number for each band identified in panel A.

    Journal: Applied and Environmental Microbiology

    Article Title: Molecular Monitoring of Succession of Bacterial Communities in Human Neonates

    doi: 10.1128/AEM.68.1.219-226.2002

    Figure Lengend Snippet: (A) PCR-DGGE profiles representing the bacterial diversity in baby D generated from samples taken from birth to 323 days. Both the day and the approximate time of the month of sampling are indicated. Changes in the diet are indicated by arrows. The bands identified from the 16S rDNA clone libraries are numbered and are indicated by arrowheads; these bands are described in the table in panel B. (B) Closest relative as determined by comparative sequence analysis, level of identity with this relative, clone designation, and accession number for each band identified in panel A.

    Article Snippet: PCR fragments, also called amplicons, were separated by DGGE by using the specifications of Muyzer et al. ( ) and the Decode system (Bio-Rad Laboratories, Hercules, Calif.), with the following modifications.

    Techniques: Polymerase Chain Reaction, Denaturing Gradient Gel Electrophoresis, Generated, Sampling, Sequencing

    A. PCR screening, using primers P1D and P1test, of plaques obtained upon phage recombineering. Lanes 4 and 11 contain PCR products that indicate the presence of P1virΔIS within the plaques. B. PCR verification of the shortening of the IS‐deleted region in a pure P1virΔIS lysate using primers P1D and P1 BP. M: 1 kb DNA ladder (Fermentas).

    Journal: Microbial biotechnology

    Article Title: Bacteriophage recombineering in the lytic state using the lambda red recombinases

    doi: 10.1111/j.1751-7915.2011.00292.x

    Figure Lengend Snippet: A. PCR screening, using primers P1D and P1test, of plaques obtained upon phage recombineering. Lanes 4 and 11 contain PCR products that indicate the presence of P1virΔIS within the plaques. B. PCR verification of the shortening of the IS‐deleted region in a pure P1virΔIS lysate using primers P1D and P1 BP. M: 1 kb DNA ladder (Fermentas).

    Article Snippet: A mixture containing 100 ng of phage DNA and 300 ng of the P1AP–P1 BP PCR fragment was electroporated into an aliquot of MG1655/pKD46 cells at a voltage of 1800 V in a 0.1 cm electroporation cuvette using a Bio‐Rad MicroPulser Electroporator.

    Techniques: Polymerase Chain Reaction