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cy3  (Danaher Inc)


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    Structured Review

    Danaher Inc cy3
    Cy3, supplied by Danaher Inc, used in various techniques. Bioz Stars score: 96/100, based on 807 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/fairplay+microarray+labelling+kit/Cy3-dCTP/pmc05552732-210-6-10
    Average 96 stars, based on 807 article reviews
    cy3 - by Bioz Stars, 2026-11
    96/100 stars

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    Related Articles

    other:

    Article Title: Array comparative hybridisation reveals a high degree of similarity between UK and European clinical isolates of hypervirulent Clostridium difficile
    Article Snippet: The genomic DNA was labelled using the Bioprime DNA labelling system (Invitrogen, UK).

    Labeling:

    Article Title: Genotypic and Phenotypic Modifications of Neisseria meningitidis after an Accidental Human Passage
    Article Snippet: .. Equal amounts of RNAs of each strain were labeled differentially using Cy3-dCTP and Cy5-dCTP (Amersham Pharmacia) during a first reverse-transcriptase step using the Superscript II RNase H− reverse transcriptase (Life Technologies) and a balanced mixture (20 pmol each) of C-terminal primers specific for each gene present on the microarrays. .. The differentially labeled cDNA were combined and hybridized overnight at 42°C to the Neisseria chips (Eurogentec), composed of overlapping 40-mer oligonucleotides covering the entire genome of strain Z2491.

    Article Title: Alternative sigma factor σ H activates competence gene expression in Lactobacillus sakei
    Article Snippet: Each oligonucleotide was spotted in triplicate on UltraGaps coated slides (Corning ® Life Sciences). .. Total RNA (5 μg) was reverse transcribed and labeled with either Cy5 dCTP or Cy3 dCTP (Amersham Biosciences) using the ChipShotTM Direct Labeling System (Promega). .. Labelled cDNA (50 pmol of Cy3 and 50 pmol of Cy5) was included in a dye-switch hybridization protocol carried out in an automatic hybridization chamber (Discovery, Ventana Medical system).

    Reverse Transcription:

    Article Title: Genotypic and Phenotypic Modifications of Neisseria meningitidis after an Accidental Human Passage
    Article Snippet: .. Equal amounts of RNAs of each strain were labeled differentially using Cy3-dCTP and Cy5-dCTP (Amersham Pharmacia) during a first reverse-transcriptase step using the Superscript II RNase H− reverse transcriptase (Life Technologies) and a balanced mixture (20 pmol each) of C-terminal primers specific for each gene present on the microarrays. .. The differentially labeled cDNA were combined and hybridized overnight at 42°C to the Neisseria chips (Eurogentec), composed of overlapping 40-mer oligonucleotides covering the entire genome of strain Z2491.

    Article Title: Alternative sigma factor σ H activates competence gene expression in Lactobacillus sakei
    Article Snippet: Each oligonucleotide was spotted in triplicate on UltraGaps coated slides (Corning ® Life Sciences). .. Total RNA (5 μg) was reverse transcribed and labeled with either Cy5 dCTP or Cy3 dCTP (Amersham Biosciences) using the ChipShotTM Direct Labeling System (Promega). .. Labelled cDNA (50 pmol of Cy3 and 50 pmol of Cy5) was included in a dye-switch hybridization protocol carried out in an automatic hybridization chamber (Discovery, Ventana Medical system).

    Sonication:

    Article Title: Transcriptomic profiling revealed FZD10 as a novel biomarker for nasopharyngeal carcinoma recurrence
    Article Snippet: .. In brief, 3 μg of DNA were sonicated before being combined with 5 μg of random hexamers (Roche, Madison, WI, USA), 200 μM of dATP/dGTP/dTTP, 100 g of dCTP, 60 g of Cy3-dCTP (GE Healthcare, Little Chalfont, UK), and 10 units of Klenow Fragment (exo-) (Fermentas, Madison, WI, USA) and incubated at 37°C for an overnight period. .. Cy3-labeled DNA was purified with PCR purification Kit (Qiagen, Valencia, CA, USA).

    Incubation:

    Article Title: Transcriptomic profiling revealed FZD10 as a novel biomarker for nasopharyngeal carcinoma recurrence
    Article Snippet: .. In brief, 3 μg of DNA were sonicated before being combined with 5 μg of random hexamers (Roche, Madison, WI, USA), 200 μM of dATP/dGTP/dTTP, 100 g of dCTP, 60 g of Cy3-dCTP (GE Healthcare, Little Chalfont, UK), and 10 units of Klenow Fragment (exo-) (Fermentas, Madison, WI, USA) and incubated at 37°C for an overnight period. .. Cy3-labeled DNA was purified with PCR purification Kit (Qiagen, Valencia, CA, USA).

    Concentration Assay:

    Article Title: Dynamic Profile of the Yak Mammary Transcriptome during the Lactation Cycle
    Article Snippet: The cDNA product was purified using a PCR NucleoSpin Extract II Kit (Macherey-Nagel, Düren, Germany) and vacuum-evaporated to 14 μL. .. The cDNA was mixed with 4 μg random nanomer, heated to 95 °C for 3 min, and snap-cooled on ice for 5 min. Then, 5 μL Klenow buffer, dNTP, and Cy3-dCTP (GE Healthcare) were added to a final concentration of 240 μM dATP, 240 μM dGTP, 240 μM dTTP, 120 μM dCTP, and 40 μM Cy-dCTP, followed by addition of 1.2 μL of the Klenow enzyme. ..

    Polymerase Chain Reaction:

    Article Title: Reliable Single Cell Array CGH for Clinical Samples
    Article Snippet: .. For each sample two 50μl PCR reactions were run in parallel each comprising 5 μl of 10x Expanded Long Template Buffer 1 (Roche Diagnostics), 2.4 μM of the universal primer (LIB1 or MseLig-21, depending on the adapter sequence incorporated in the WGA product), 350 μM of dATP and dGTP, 315 μM of dCTP and dTTP, 35 μM of Cy5/Cy3-dCTP and Cy5/Cy3-dUTP (GE Healthcare), 0.5 μl of BSA (Roche Diagnostics), 7.5 U of Expand-Long-Template DNA Polymerase (Roche) and 0.5 μl of the template DNA. ..

    Article Title: Sensitivity and fidelity of DNA microarray improved with integration of Amplified Differential Gene Expression (ADGE)
    Article Snippet: .. To generate the probe of HL60 DNA, a PCR reaction was set up with 0.5 μl of the reassociated DNA, 5 μl of 10x Clontech PCR buffer, 1 μl of dNTPS (10 mM dATP, dTTP, and dGTP each, 6 mM dCTP), 4 μl of FluoroLink Cy3-dCTP (Amersham Pharmacia), 4.5 μl of 10 μM CT primer, 1 μl of Clontech cDNA polymerase and 34 μl of ddH 2 O. ..

    Sequencing:

    Article Title: Reliable Single Cell Array CGH for Clinical Samples
    Article Snippet: .. For each sample two 50μl PCR reactions were run in parallel each comprising 5 μl of 10x Expanded Long Template Buffer 1 (Roche Diagnostics), 2.4 μM of the universal primer (LIB1 or MseLig-21, depending on the adapter sequence incorporated in the WGA product), 350 μM of dATP and dGTP, 315 μM of dCTP and dTTP, 35 μM of Cy5/Cy3-dCTP and Cy5/Cy3-dUTP (GE Healthcare), 0.5 μl of BSA (Roche Diagnostics), 7.5 U of Expand-Long-Template DNA Polymerase (Roche) and 0.5 μl of the template DNA. ..

    Whole Genome Amplification:

    Article Title: Reliable Single Cell Array CGH for Clinical Samples
    Article Snippet: .. For each sample two 50μl PCR reactions were run in parallel each comprising 5 μl of 10x Expanded Long Template Buffer 1 (Roche Diagnostics), 2.4 μM of the universal primer (LIB1 or MseLig-21, depending on the adapter sequence incorporated in the WGA product), 350 μM of dATP and dGTP, 315 μM of dCTP and dTTP, 35 μM of Cy5/Cy3-dCTP and Cy5/Cy3-dUTP (GE Healthcare), 0.5 μl of BSA (Roche Diagnostics), 7.5 U of Expand-Long-Template DNA Polymerase (Roche) and 0.5 μl of the template DNA. ..



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    Image Search Results


    Composite images of ADGE microarray and regular microarray. The clones corresponding to the contiguous area of twelve spots (3 × 4) were amplified by using PCR with the primers having a Taq I site at the end. After cut with Taq I , the same amount of DNA for each clone was ligated to the CT and TT adapters. The CT and TT adapter-linked DNA fragments were mixed in ratios of 1:1 for the three clones of the first column, 1:2 for the clones of the second column, 1:3 for the clones of the third column, 1:4 for the clones of the fourth column. The top panel is the result of ADGE microarray while the bottom panel is the result of regular microarray. The ratios are represented by Cy5 (green) to Cy3 (red) and normalized with the value of clones in the first column. The detected ratios are averages of three spots in each column.

    Journal: BMC Genomics

    Article Title: Sensitivity and fidelity of DNA microarray improved with integration of Amplified Differential Gene Expression (ADGE)

    doi: 10.1186/1471-2164-4-28

    Figure Lengend Snippet: Composite images of ADGE microarray and regular microarray. The clones corresponding to the contiguous area of twelve spots (3 × 4) were amplified by using PCR with the primers having a Taq I site at the end. After cut with Taq I , the same amount of DNA for each clone was ligated to the CT and TT adapters. The CT and TT adapter-linked DNA fragments were mixed in ratios of 1:1 for the three clones of the first column, 1:2 for the clones of the second column, 1:3 for the clones of the third column, 1:4 for the clones of the fourth column. The top panel is the result of ADGE microarray while the bottom panel is the result of regular microarray. The ratios are represented by Cy5 (green) to Cy3 (red) and normalized with the value of clones in the first column. The detected ratios are averages of three spots in each column.

    Article Snippet: Regular microarray was carried out following the manufacturer's instructions for the FairPlay™ microarray labeling kit (Stratagene, La Jolla, CA).

    Techniques: Microarray, Clone Assay, Amplification

    Relationship between detected ratios (y) and input ratios (x). The relationship is y = 1.05x 1.55 with R 2 = 0.97 for ADGE microarray while it is y = 0.56x +0.39 with R 2 = 0.96 for regular microarray within the input ratio of 4 (panel A). Within the input ratio range of 1~20, the relationship is y = 15.99ln(x) - 6.14 with R 2 = 0.84 for ADGE-microarray (panel B).

    Journal: BMC Genomics

    Article Title: Sensitivity and fidelity of DNA microarray improved with integration of Amplified Differential Gene Expression (ADGE)

    doi: 10.1186/1471-2164-4-28

    Figure Lengend Snippet: Relationship between detected ratios (y) and input ratios (x). The relationship is y = 1.05x 1.55 with R 2 = 0.97 for ADGE microarray while it is y = 0.56x +0.39 with R 2 = 0.96 for regular microarray within the input ratio of 4 (panel A). Within the input ratio range of 1~20, the relationship is y = 15.99ln(x) - 6.14 with R 2 = 0.84 for ADGE-microarray (panel B).

    Article Snippet: Regular microarray was carried out following the manufacturer's instructions for the FairPlay™ microarray labeling kit (Stratagene, La Jolla, CA).

    Techniques: Microarray

    The MA plots of ADGE microarray and regular microarray. A is the average of log 2 Cy5 and log 2 Cy3, representing intensities of spots. M is the difference of log 2 Cy5 and log 2 Cy3, representing the expression ratios in the power of 2, with positive values for up-regulated genes, negative values for down-regulated genes and 0 for unchanged genes. Panel A: ADGE microarray with HL60 vs HL60/TLK286, average of three replicates. Panel B: regular microarray with HL60 vs HL60/TLK286, average of three replicates. Panel C: ADGE microarray with HL60 vs HL60, average of two replicates. Panel D: number of differential genes selected from all genes on the chip or from genes with > 99% confidence level.

    Journal: BMC Genomics

    Article Title: Sensitivity and fidelity of DNA microarray improved with integration of Amplified Differential Gene Expression (ADGE)

    doi: 10.1186/1471-2164-4-28

    Figure Lengend Snippet: The MA plots of ADGE microarray and regular microarray. A is the average of log 2 Cy5 and log 2 Cy3, representing intensities of spots. M is the difference of log 2 Cy5 and log 2 Cy3, representing the expression ratios in the power of 2, with positive values for up-regulated genes, negative values for down-regulated genes and 0 for unchanged genes. Panel A: ADGE microarray with HL60 vs HL60/TLK286, average of three replicates. Panel B: regular microarray with HL60 vs HL60/TLK286, average of three replicates. Panel C: ADGE microarray with HL60 vs HL60, average of two replicates. Panel D: number of differential genes selected from all genes on the chip or from genes with > 99% confidence level.

    Article Snippet: Regular microarray was carried out following the manufacturer's instructions for the FairPlay™ microarray labeling kit (Stratagene, La Jolla, CA).

    Techniques: Microarray, Expressing

    The variances of Cy3 (HL60) (panel A) and Cy5 (HL60/TLK286) (panel B) in ADGE microarray and regular microarray. The normalized values of Cy3 and Cy5 were used to calculate the variances. Panel C is the number of genes with confidence levels of 90% or greater in ADGE microarray and regular microarray. The confidence level is a result of t-test for each gene.

    Journal: BMC Genomics

    Article Title: Sensitivity and fidelity of DNA microarray improved with integration of Amplified Differential Gene Expression (ADGE)

    doi: 10.1186/1471-2164-4-28

    Figure Lengend Snippet: The variances of Cy3 (HL60) (panel A) and Cy5 (HL60/TLK286) (panel B) in ADGE microarray and regular microarray. The normalized values of Cy3 and Cy5 were used to calculate the variances. Panel C is the number of genes with confidence levels of 90% or greater in ADGE microarray and regular microarray. The confidence level is a result of t-test for each gene.

    Article Snippet: Regular microarray was carried out following the manufacturer's instructions for the FairPlay™ microarray labeling kit (Stratagene, La Jolla, CA).

    Techniques: Microarray

    Comparison of ADGE  microarray  results between two duplicated spots

    Journal: BMC Genomics

    Article Title: Sensitivity and fidelity of DNA microarray improved with integration of Amplified Differential Gene Expression (ADGE)

    doi: 10.1186/1471-2164-4-28

    Figure Lengend Snippet: Comparison of ADGE microarray results between two duplicated spots

    Article Snippet: Regular microarray was carried out following the manufacturer's instructions for the FairPlay™ microarray labeling kit (Stratagene, La Jolla, CA).

    Techniques: Microarray

    Illustration of the microarray experiment. The various steps of the experiment and the corresponding covariates used in the model are listed with their symbols. The model consists of three levels: (i) selection, (ii) scanning and (iii) measurement. In (i), K g 1 and K g 2 mRNA molecules for gene g present in sample 1 and 2 undergo a selection process. Each molecule succeeds or fails in each of the experimental steps: cDNA synthesis, dye labelling, purification, hybridization and washing. Success for each molecule is modelled as a Bernoulli coin toss. The success probability depends on properties of the molecule and of the experiment (covariates). Molecules of the same gene can have different covariates, e.g. if they hybridize on different spots with different probes. If probe is in excess, molecules can be modelled as independent variables and the number of remaining molecules after each step is binomially distributed. The probability of successfully passing through the entire experiment is the product of the probabilities of surviving each individual step. Nested binomial variables are binomial and the final number of molecules ready for being scanned is binomial with two parameters: the unknown original number of transcripts per gene in each sample and the selection probability, modelled as in . Level (ii) describes the translation of the bound molecules remaining after washing ( H s t , a , on array a , spot s , for sample t = 1, 2) into fluorescence intensities, as in . Measurement error (iii) of pixel-wise intensities L j , s t , a (on array a , pixel j on spot s for sample t = 1, 2) is assumed to be normally distributed as in . This model allows to obtain estimates of absolute concentrations K g 1 and K g 2 together with their posterior marginal probability density, as sketched at the bottom.

    Journal: Nucleic Acids Research

    Article Title: Genome-wide estimation of transcript concentrations from spotted cDNA microarray data

    doi: 10.1093/nar/gni141

    Figure Lengend Snippet: Illustration of the microarray experiment. The various steps of the experiment and the corresponding covariates used in the model are listed with their symbols. The model consists of three levels: (i) selection, (ii) scanning and (iii) measurement. In (i), K g 1 and K g 2 mRNA molecules for gene g present in sample 1 and 2 undergo a selection process. Each molecule succeeds or fails in each of the experimental steps: cDNA synthesis, dye labelling, purification, hybridization and washing. Success for each molecule is modelled as a Bernoulli coin toss. The success probability depends on properties of the molecule and of the experiment (covariates). Molecules of the same gene can have different covariates, e.g. if they hybridize on different spots with different probes. If probe is in excess, molecules can be modelled as independent variables and the number of remaining molecules after each step is binomially distributed. The probability of successfully passing through the entire experiment is the product of the probabilities of surviving each individual step. Nested binomial variables are binomial and the final number of molecules ready for being scanned is binomial with two parameters: the unknown original number of transcripts per gene in each sample and the selection probability, modelled as in . Level (ii) describes the translation of the bound molecules remaining after washing ( H s t , a , on array a , spot s , for sample t = 1, 2) into fluorescence intensities, as in . Measurement error (iii) of pixel-wise intensities L j , s t , a (on array a , pixel j on spot s for sample t = 1, 2) is assumed to be normally distributed as in . This model allows to obtain estimates of absolute concentrations K g 1 and K g 2 together with their posterior marginal probability density, as sketched at the bottom.

    Article Snippet: Labelled cDNA was synthesized from 20 µg total RNA using Superscript II transcriptase (Life technologies) and Fairplay Microarray Labeling kit (Stratagene) in the presence of either Cy3-dUTP or Cy5-dUTP (Amersham Pharmacia).

    Techniques: Microarray, Selection, Purification, Hybridization, Fluorescence

    Validation of the microarray results . The transcriptomic results obtained by microarray hybridisation were validated by quantitive RT-PCR (qRT-PCR) analysis. The level of differential expression of 12 genes was compared and showed a correlation between microarray (Y-axis) and qRT-PCR analysis (X-axis). The level of differential expression between iron replete and iron limitation is given in Log 2 -values.

    Journal: BMC Genomics

    Article Title: Investigation of the human pathogen Acinetobacter baumannii under iron limiting conditions

    doi: 10.1186/1471-2164-12-126

    Figure Lengend Snippet: Validation of the microarray results . The transcriptomic results obtained by microarray hybridisation were validated by quantitive RT-PCR (qRT-PCR) analysis. The level of differential expression of 12 genes was compared and showed a correlation between microarray (Y-axis) and qRT-PCR analysis (X-axis). The level of differential expression between iron replete and iron limitation is given in Log 2 -values.

    Article Snippet: Total RNA was reverse transcribed and labelled with either Cy3 or Cy5 using the Agilent Fairplay Microarray Labelling kit (Stratagene).

    Techniques: Microarray, Hybridization, Reverse Transcription Polymerase Chain Reaction, Quantitative RT-PCR, Expressing

    Microarray results displayed by COG-function . Depiction of cluster of orthologous groups (COG) and the percentage of up-regulated (green) and down-regulated genes (red) within such group determined by microarray. The total number of genes per COG is shown in parentheses.

    Journal: BMC Genomics

    Article Title: Investigation of the human pathogen Acinetobacter baumannii under iron limiting conditions

    doi: 10.1186/1471-2164-12-126

    Figure Lengend Snippet: Microarray results displayed by COG-function . Depiction of cluster of orthologous groups (COG) and the percentage of up-regulated (green) and down-regulated genes (red) within such group determined by microarray. The total number of genes per COG is shown in parentheses.

    Article Snippet: Total RNA was reverse transcribed and labelled with either Cy3 or Cy5 using the Agilent Fairplay Microarray Labelling kit (Stratagene).

    Techniques: Microarray

    The effect of NaCl on the expression of EF0282, EF1211 and EF2642 as quantified by QPCR (□; Pfaffl method), and by microarray (▪).

    Journal: PLoS ONE

    Article Title: Transcriptomic and Functional Analysis of NaCl-Induced Stress in Enterococcus faecalis

    doi: 10.1371/journal.pone.0094571

    Figure Lengend Snippet: The effect of NaCl on the expression of EF0282, EF1211 and EF2642 as quantified by QPCR (□; Pfaffl method), and by microarray (▪).

    Article Snippet: The concentrations of the RNA samples were measured by using the NanoDrop (NanoDrop Technologies), and the quality was assessed by using the RNA 600 Nano LabChip kit and the Bioanalyzer 2100 (Agilent Technologies). cDNA was synthesized and labeled with the Fairplay II Microarray labeling kit (Stratagene), with modifications as previously described .

    Techniques: Expressing, Microarray