AFFYMETRIX CHIP PROCESSING AND SCANNING
The Affymetrix platform uses GeneChips-arrays enclosed by a pre-fabricated casing to minimize handling and variability among hybridizations. Each Affymetrix array is synthesized on a square of silicon that ranges in size from a few millimeters a side to about a cm on each edge. Solutions such as hybridization and wash buffers are introduced through one of two rubber septa located on the back of the genechip.
Genechips are loaded with the labeled target in hybridization buffer and incubated overnight in a rotating oven at 60rpm and a set temperature which varies depending upon the type of the array. After hybridization, the buffer and labeled target are removed from the chip and stored in case future hybridizations are desired for that sample. These hybridization cocktails are good for several additional hybridizations.
After removing the Hybridization cocktail, chips are loaded into the Affymetrix Fluidics Station, an automated array processing robot that washes each chip with a pre-set series of buffers and temperature combinations. The chips are then loaded with streptavidin conjugated to phycoerythyrin, to allow fluorescent detection of hybridized target.
The Genechips are next placed in the GeneChip Scanner 3000, which scans the chips at a resolution of less than 2 microns. The data generated is checked for overall quality, both visually and by inspection of qc metrics, and saved to the researcher's account on our servers.