![]() ![]() Approximately 20 probes, predicted to perform well by in silico metrics, are chosen randomly from a tiling database and printed on the array in triplicate.Probes designed against endogenous “species-specific” sequence can be used to measure hybridization and wash stringency.Deletion stringency probes ( e.g., DCP_008001.0).Common practice is to have this probe highly replicated.This is the same probe sequence used as the BrightCorner probe. Endogenous “species-specific” sequences predicted to have high signal, due to multiple copies found in the targeted genome, are used as positive controls.They do not show significant signal from any sample tested. There are currently 12 sequences replicated 40 times marked as control type Positive that are reserved negative controls for future potential use as positive controls.Common practice is to have one highly replicated NC probe (>100) and the other NC probes at lower replication (≈6).Currently there are 82 different negative control NC probes.These probes are used to estimate on element background. These are probes shown not to have significant signal from any sample tested.This probe forms a hairpin and does not hybridize well with labeled sample of any species Usually highly replicated on the array used to measure on element background.These probes are the same as the 3xSLv1 probes described below.These, along with the bright corner probes, make up the corner-specific patterns. Used for orientation purposes in the array corners.These probes are predicted to have high signal due to the multiple copies found in the genome. These probes are designed to endogenous sequence and are thus species-specific.These probes are placed in the corners of the array with a different pattern for each corner. The negative control probes are used to measure on element background.īelow are some of the probe types you can expect to find on a species-specific genomic control grid. Since they lack endogenous positive control probes, genomic control grids can be used for any species. The “genomic” control grids are generic grids that contain only negative controls. Positive controls can be used for image orientation and to assess whether the sample was labeled. These grids contain positive controls probes that were designed against the endogenous sequence for the species. For every microarray design format and species, Agilent has a default species-specific control grid. A control grid is a set of control probes that SureDesign adds to every microarray design. ![]()
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