Journal: BMC Bioinformatics

Article Title: Characterization and simulation of cDNA microarray spots using a novel mathematical model

doi: 10.1186/1471-2105-8-485

Figure Lengend Snippet: Simulated cDNA deposit in various shapes . By varying parameters x 0 , K , a , and K V with three different values, we obtained a total of 81 different shapes of cDNA deposit. The values of parameters used for simulating each shape of cDNA deposit are listed in the tables on the left and the bottom of the image.

Article Snippet: While homemade poly-L-lysine-coated glass slides have been widely used, several commercial microarray slides are now preferred, such as the FMB cDNA slide (Full Moon Biosystems Inc.), ArrayIt SuperAmine and SuperAldehyde slides (TeleChem International, Inc.).

Techniques:

Journal: BMC Bioinformatics

Article Title: Characterization and simulation of cDNA microarray spots using a novel mathematical model

doi: 10.1186/1471-2105-8-485

Figure Lengend Snippet: Three types of morphology of simulated cDNA deposit . (A) The doughnut-shaped spot was generated with x 0 = 1000, K = 0.002, a = 0.4, and K V = 2.0. (B) The peak-shaped spot was generated with x 0 = 300, K = 0.001, a = 0.4, and K V = 3.0. (C) The volcano-shaped spot was generated with x 0 = 1000, K = 0.0005, a = -0.4, K V = 3.0, and. Here, mean, median and mode are the arithmetic mean, the value of the middle term ranked in increasing order, and the value that occurs with the highest frequency, respectively.

Article Snippet: While homemade poly-L-lysine-coated glass slides have been widely used, several commercial microarray slides are now preferred, such as the FMB cDNA slide (Full Moon Biosystems Inc.), ArrayIt SuperAmine and SuperAldehyde slides (TeleChem International, Inc.).

Techniques: Generated

Journal: BMC Bioinformatics

Article Title: Characterization and simulation of cDNA microarray spots using a novel mathematical model

doi: 10.1186/1471-2105-8-485

Figure Lengend Snippet: Simulated cDNA deposit . From the profile of cDNA deposits and the spot template images, the cDNA deposit was simulated. (A) We set ( x i , y i ), the coordinates of pixels on the edge contour, where i = 1, 2,..., n ; ( C x , C y ), centre of the spot area; R i , the distance from the centre to the i th pixel on the edge contour; and r ij , the distance from the centre to each pixel in the spot area, where j = 0, 1,..., R i . (B) The 3D images of the deposited cDNA were visualized.

Article Snippet: While homemade poly-L-lysine-coated glass slides have been widely used, several commercial microarray slides are now preferred, such as the FMB cDNA slide (Full Moon Biosystems Inc.), ArrayIt SuperAmine and SuperAldehyde slides (TeleChem International, Inc.).

Techniques: