Glass Slide hybridization and Scanning
Many kinds of arrays, including those of Agilent, are printed or synthesized on 1" by 3" glass slides. The CAT is equipped to hybridize and process most kinds of glass slides. For Agilent, hybridization is done using Agilent's oligo hybridization kit and their stainless steel slide hybridization chambers.
With these chambers, a rubber-gasketed coverslip is first set into one half of the slide holder. The hybridization buffer containing the labeled target is pipetted onto the coverslip and the array is lowered down onto the coverslip, sandwiching the hybridization solution in between. The second half of the slide holder is then lowered onto the slide/coverslip sandwich and clamped tightly. The assembled slide holder is then placed in a rotating oven set at 60 degrees Celsius for the over night incubation.
The next day, the slide holders are removed from the oven and carefully disassembled. The slide/coverslip sandwich is submerged in wash buffer and then teased gently apart. All the slides are placed in glass slide holders and washed according to Agilent's protocol. Slides are then dried with a stream of nitrogen and placed in the Agilent scanner. After scanning, the intensities of the array features are determined using Agilent's Feature Extractor software, and the resulting text files deposited in the researcher's account on our server.