Washing staining and scanning

After hybridization, the probe array is subjected to a series of washes in the fluidics station. Stringent and non-stringent washes are specifically optimized for each probe array type. The hybridized and washed probe arrays are next stained with strepavidin-phycoerythrin conjugate. Please check the fluidics protocol(s) required for the array type you are using on the information sheet provided for each Affymetrix probe array type.

The Affymetrix GeneChip® fluidics station is used for array washing, staining and signal amplification. Place water, washing buffers, SAPE solution and antibody solution in the fluidics station. Refer to the user manual for handling the fluidics station.

After completion of the wash program, check the probe array window for air bubbles. To remove air bubbles, insert a clean pipette tip into the upper septum of the array. Keep the array in a vertical position and pipette 200 | l non-stringent wash buffer into the array using the lower septum of the array. Pipette another 150 |l buffer into the array (extra buffer will come out through the pipette tip attached to the upper septum). Keep the probe arrays without air bubbles at 4°C in the dark until scanning. Refer to the instructions of the scanner and the operating software for scanning. Each complete array image is stored in a separate raw data file (*.dat). The GeneChip® operating software analyzes the image files and derives a single intensity value for each probe cell of an array. These values are contained in the cell intensity (*.cel) file.

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