The quartz wafer is in the holding position on the DNA synthesizer. The wafer is moved to a vertical reaction vessel for the process of DNA chain elongation.
A technician uses a computer guiding system to align the filter mask in perfect register with the quartz wafer. The filter mask will block light to selected regions of the wafer. More nucleotides can be added to the exposed regions.
Here you can see a technician shuttling a quartz wafer (containing 50-400 GeneChips) between alternating photolithography and DNA synthesis steps.
A technician loads a quartz wafer into the DNA synthesizer, where nucleotides will be added to selected sequences to build probes.
Affymetrix, the makers of GeneChip arrays.