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fairplay iii microarray labeling kit  (Agilent technologies)


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    Agilent technologies fairplay iii microarray labeling kit
    Fairplay Iii Microarray Labeling Kit, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/fairplay+microarray+labelling+kit/pmc03517412-184-9-14
    Average 90 stars, based on 1 article reviews
    fairplay iii microarray labeling kit - by Bioz Stars, 2026-09
    90/100 stars

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    Related Articles

    Labeling:

    Article Title: The Transcriptional Heat Shock Response of Salmonella Typhimurium Shows Hysteresis and Heated Cells Show Increased Resistance to Heat and Acid Stress
    Article Snippet: The quality of the RNA was checked using the NanoDrop (Fisher Scientific, Slangerup, Denmark). .. Labeled cDNA was synthesized from total RNA using the FairPlay III Microarray Labeling Kit (Agilent Technologies, Hoersholm, Denmark) according to manufacturer’s instructions without the Spike-in step. cDNA from the untreated cultures was labeled with Cy5 and cDNA from the stressed culture was labeled with Cy3. .. The labeled cDNA from the two cultures were mixed together and competitively hybridized on an 8×15 K Agilent microarray slide constructed for Salmonella Typhimurium strain SL1344 (deposited with GEO database ref. number: GPL15227) at 65°C for 17 hours, washed and scanned according to the “Two-Color Microarray-Based Prokaryote Analysis Protocol” (Agilent Technologies).

    Article Title: Characterization of the YdeO Regulon in Escherichia coli
    Article Snippet: .. We used the FairPlay III Microarray Labeling kit (Agilent), CyDye Cy3 mono-reactive Dye, and CyDye Cy5 mono-reactive Dye (GE Healthcare). ..

    Article Title: Global Transcriptome Analysis of Lactococcus garvieae Strains in Response to Temperature
    Article Snippet: .. A total of 5 μg of total RNA of each sample replicate was reverse transcripted and labeled by using the FairPlay III Labeling Kit (Agilent Technologies) according to the protocol provided by the manufacturer except for the following: purification of the dye-coupled cDNA was performed by using QIAquick PCR purification kit (Qiagen). .. The yield and the specific activity of each labeling reaction were determined in a NanoDrop 1000 spectrophotometer (NanoDrop Technologies, Inc., Rockland, DE).

    Article Title: Tumorigenic Properties of Iron Regulatory Protein 2 (IRP2) Mediated by Its Specific 73-Amino Acids Insert
    Article Snippet: .. Total RNA (5 μg) was reverse transcribed using the Fairplay III Microarray Labeling kit (Stratagene) and labeled with Cy3-dCTP or Cy5-dCTP. .. Following clean-up using Fairplay columns (Stratagene), labeled cDNA and universal reference (Stratagene) were combined and hybridized to a 4×44K two-color gene expression array (Agilent Technologies).

    Article Title: AmyR Is a Novel Negative Regulator of Amylovoran Production in Erwinia amylovora
    Article Snippet: .. Ten μg of total RNA from each sample were reverse transcribed and labeled by Alexa Fluor dye 555 using the FairPlay III Microarray Labeling Kit (Stratagene, La Jolla, CA, USA) according to manufacturer's instruction, except that purification steps were done using the QIAquick PCR Purification Kit (Qiagen, Hilden, Germany). .. Microarray hybridization was performed using 600 ng dye-labeled cDNA in the presence of a 2× Hybridization Buffer (Agilent Technologies, Palo Alto, CA, USA) for 17 h at 65°C in an Agilent rotating oven (10 rpm).

    Article Title: Broad Epigenetic Signature of Maternal Care in the Brain of Adult Rats
    Article Snippet: RNA spike-in controls (Agilent) were added to RNA prior to generating cDNA. .. The cDNA was amplified and labeled with Cy3 or Cy5 (GE Healthcare) according to manufacturer's instructions (Fairplay III, Agilent; See for details). ..

    Article Title: Microarray analysis of Shigella flexneri -infected epithelial cells identifies host factors important for apoptosis inhibition
    Article Snippet: .. The FairPlay III kit (Stratagene) was used for preparing labeled cDNA with some modifications. ..

    Article Title: Extracytoplasmic function (ECF) sigma factor σ F is involved in Caulobacter crescentus response to heavy metal stress
    Article Snippet: PCR products were ligated into the pGEM-T vector (Promega) and several distinct clones were sequenced. .. Three distinct biological RNA samples isolated from each strain analyzed were reverse transcribed and labeled using the FairPlay III Microarray Labeling system (Agilent). ..

    Synthesized:

    Article Title: The Transcriptional Heat Shock Response of Salmonella Typhimurium Shows Hysteresis and Heated Cells Show Increased Resistance to Heat and Acid Stress
    Article Snippet: The quality of the RNA was checked using the NanoDrop (Fisher Scientific, Slangerup, Denmark). .. Labeled cDNA was synthesized from total RNA using the FairPlay III Microarray Labeling Kit (Agilent Technologies, Hoersholm, Denmark) according to manufacturer’s instructions without the Spike-in step. cDNA from the untreated cultures was labeled with Cy5 and cDNA from the stressed culture was labeled with Cy3. .. The labeled cDNA from the two cultures were mixed together and competitively hybridized on an 8×15 K Agilent microarray slide constructed for Salmonella Typhimurium strain SL1344 (deposited with GEO database ref. number: GPL15227) at 65°C for 17 hours, washed and scanned according to the “Two-Color Microarray-Based Prokaryote Analysis Protocol” (Agilent Technologies).

    Microarray:

    Article Title: The Transcriptional Heat Shock Response of Salmonella Typhimurium Shows Hysteresis and Heated Cells Show Increased Resistance to Heat and Acid Stress
    Article Snippet: The quality of the RNA was checked using the NanoDrop (Fisher Scientific, Slangerup, Denmark). .. Labeled cDNA was synthesized from total RNA using the FairPlay III Microarray Labeling Kit (Agilent Technologies, Hoersholm, Denmark) according to manufacturer’s instructions without the Spike-in step. cDNA from the untreated cultures was labeled with Cy5 and cDNA from the stressed culture was labeled with Cy3. .. The labeled cDNA from the two cultures were mixed together and competitively hybridized on an 8×15 K Agilent microarray slide constructed for Salmonella Typhimurium strain SL1344 (deposited with GEO database ref. number: GPL15227) at 65°C for 17 hours, washed and scanned according to the “Two-Color Microarray-Based Prokaryote Analysis Protocol” (Agilent Technologies).

    Article Title: Characterization of the YdeO Regulon in Escherichia coli
    Article Snippet: .. We used the FairPlay III Microarray Labeling kit (Agilent), CyDye Cy3 mono-reactive Dye, and CyDye Cy5 mono-reactive Dye (GE Healthcare). ..

    Article Title: Tumorigenic Properties of Iron Regulatory Protein 2 (IRP2) Mediated by Its Specific 73-Amino Acids Insert
    Article Snippet: .. Total RNA (5 μg) was reverse transcribed using the Fairplay III Microarray Labeling kit (Stratagene) and labeled with Cy3-dCTP or Cy5-dCTP. .. Following clean-up using Fairplay columns (Stratagene), labeled cDNA and universal reference (Stratagene) were combined and hybridized to a 4×44K two-color gene expression array (Agilent Technologies).

    Article Title: AmyR Is a Novel Negative Regulator of Amylovoran Production in Erwinia amylovora
    Article Snippet: .. Ten μg of total RNA from each sample were reverse transcribed and labeled by Alexa Fluor dye 555 using the FairPlay III Microarray Labeling Kit (Stratagene, La Jolla, CA, USA) according to manufacturer's instruction, except that purification steps were done using the QIAquick PCR Purification Kit (Qiagen, Hilden, Germany). .. Microarray hybridization was performed using 600 ng dye-labeled cDNA in the presence of a 2× Hybridization Buffer (Agilent Technologies, Palo Alto, CA, USA) for 17 h at 65°C in an Agilent rotating oven (10 rpm).

    Article Title: Extracytoplasmic function (ECF) sigma factor σ F is involved in Caulobacter crescentus response to heavy metal stress
    Article Snippet: PCR products were ligated into the pGEM-T vector (Promega) and several distinct clones were sequenced. .. Three distinct biological RNA samples isolated from each strain analyzed were reverse transcribed and labeled using the FairPlay III Microarray Labeling system (Agilent). ..

    Purification:

    Article Title: Global Transcriptome Analysis of Lactococcus garvieae Strains in Response to Temperature
    Article Snippet: .. A total of 5 μg of total RNA of each sample replicate was reverse transcripted and labeled by using the FairPlay III Labeling Kit (Agilent Technologies) according to the protocol provided by the manufacturer except for the following: purification of the dye-coupled cDNA was performed by using QIAquick PCR purification kit (Qiagen). .. The yield and the specific activity of each labeling reaction were determined in a NanoDrop 1000 spectrophotometer (NanoDrop Technologies, Inc., Rockland, DE).

    Article Title: AmyR Is a Novel Negative Regulator of Amylovoran Production in Erwinia amylovora
    Article Snippet: .. Ten μg of total RNA from each sample were reverse transcribed and labeled by Alexa Fluor dye 555 using the FairPlay III Microarray Labeling Kit (Stratagene, La Jolla, CA, USA) according to manufacturer's instruction, except that purification steps were done using the QIAquick PCR Purification Kit (Qiagen, Hilden, Germany). .. Microarray hybridization was performed using 600 ng dye-labeled cDNA in the presence of a 2× Hybridization Buffer (Agilent Technologies, Palo Alto, CA, USA) for 17 h at 65°C in an Agilent rotating oven (10 rpm).

    Polymerase Chain Reaction:

    Article Title: Global Transcriptome Analysis of Lactococcus garvieae Strains in Response to Temperature
    Article Snippet: .. A total of 5 μg of total RNA of each sample replicate was reverse transcripted and labeled by using the FairPlay III Labeling Kit (Agilent Technologies) according to the protocol provided by the manufacturer except for the following: purification of the dye-coupled cDNA was performed by using QIAquick PCR purification kit (Qiagen). .. The yield and the specific activity of each labeling reaction were determined in a NanoDrop 1000 spectrophotometer (NanoDrop Technologies, Inc., Rockland, DE).

    Article Title: AmyR Is a Novel Negative Regulator of Amylovoran Production in Erwinia amylovora
    Article Snippet: .. Ten μg of total RNA from each sample were reverse transcribed and labeled by Alexa Fluor dye 555 using the FairPlay III Microarray Labeling Kit (Stratagene, La Jolla, CA, USA) according to manufacturer's instruction, except that purification steps were done using the QIAquick PCR Purification Kit (Qiagen, Hilden, Germany). .. Microarray hybridization was performed using 600 ng dye-labeled cDNA in the presence of a 2× Hybridization Buffer (Agilent Technologies, Palo Alto, CA, USA) for 17 h at 65°C in an Agilent rotating oven (10 rpm).

    Reverse Transcription:

    Article Title: Tumorigenic Properties of Iron Regulatory Protein 2 (IRP2) Mediated by Its Specific 73-Amino Acids Insert
    Article Snippet: .. Total RNA (5 μg) was reverse transcribed using the Fairplay III Microarray Labeling kit (Stratagene) and labeled with Cy3-dCTP or Cy5-dCTP. .. Following clean-up using Fairplay columns (Stratagene), labeled cDNA and universal reference (Stratagene) were combined and hybridized to a 4×44K two-color gene expression array (Agilent Technologies).

    Article Title: AmyR Is a Novel Negative Regulator of Amylovoran Production in Erwinia amylovora
    Article Snippet: .. Ten μg of total RNA from each sample were reverse transcribed and labeled by Alexa Fluor dye 555 using the FairPlay III Microarray Labeling Kit (Stratagene, La Jolla, CA, USA) according to manufacturer's instruction, except that purification steps were done using the QIAquick PCR Purification Kit (Qiagen, Hilden, Germany). .. Microarray hybridization was performed using 600 ng dye-labeled cDNA in the presence of a 2× Hybridization Buffer (Agilent Technologies, Palo Alto, CA, USA) for 17 h at 65°C in an Agilent rotating oven (10 rpm).

    Article Title: Extracytoplasmic function (ECF) sigma factor σ F is involved in Caulobacter crescentus response to heavy metal stress
    Article Snippet: PCR products were ligated into the pGEM-T vector (Promega) and several distinct clones were sequenced. .. Three distinct biological RNA samples isolated from each strain analyzed were reverse transcribed and labeled using the FairPlay III Microarray Labeling system (Agilent). ..

    Amplification:

    Article Title: Broad Epigenetic Signature of Maternal Care in the Brain of Adult Rats
    Article Snippet: RNA spike-in controls (Agilent) were added to RNA prior to generating cDNA. .. The cDNA was amplified and labeled with Cy3 or Cy5 (GE Healthcare) according to manufacturer's instructions (Fairplay III, Agilent; See for details). ..

    Isolation:

    Article Title: Extracytoplasmic function (ECF) sigma factor σ F is involved in Caulobacter crescentus response to heavy metal stress
    Article Snippet: PCR products were ligated into the pGEM-T vector (Promega) and several distinct clones were sequenced. .. Three distinct biological RNA samples isolated from each strain analyzed were reverse transcribed and labeled using the FairPlay III Microarray Labeling system (Agilent). ..



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    Composite images of ADGE <t>microarray</t> 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.
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    fairplay microarray labeling kit  (Agilent technologies)
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    Illustration of the <t>microarray</t> 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.
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    fairplay microarray labelling kit  (Agilent technologies)
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    Validation of the <t>microarray</t> 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.
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    fairplay iii microarray labeling kit  (Agilent technologies)
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    Validation of the <t>microarray</t> 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.
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    fairplay ii microarray labeling kit  (Agilent technologies)
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    The effect of NaCl on the expression of EF0282, EF1211 and EF2642 as quantified by QPCR (□; Pfaffl method), and by <t>microarray</t> (▪).
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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