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

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

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

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

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

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

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

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

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