Mapping 250K/500K SNP assay

Pre-PCR Clean Room
PCR Staging Room
22 GeneChip ® Mapping 500K Assay Manual
• Use dedicated equipment (e.g., pipets, tips, thermocyclers, etc.) for
pre-PCR stages.
• Print separate copies of the protocol for each room.
In addition, the following areas should be used when performing this
assay: pre-PCR Clean Room, PCR Staging Room, and Main Lab. A
summary of the areas is shown in Figure 2.1.
Once you enter the Main Lab, do not return to the Pre-PCR Room or
the PCR Staging Room until you have showered and changed into
freshly laundered clothing.
The Pre-PCR Clean Room (or dedicated area such as a biosafety hood)
should be free of DNA template and PCR amplicons. The master
stocks of PCR primer and adaptor should be stored here, with aliquots
taken for use in the PCR Staging Room (or area). Reagent preparation
tasks, such as preparing master mixes, should be done in this room.
The use of gowns, booties, and gloves is strongly recommended to
prevent PCR carryover and to minimize the risk of trace levels of
contaminants being brought into the Pre-PCR Clean Area. This room
should contain dedicated pipets, tips, vortex, etc. Refer to Appendix
A or Appendix D as appropriate for more details.
The PCR Staging Room (or Area) is a low copy template lab, which
should be free from any PCR product (amplicons). It is the area where
non-amplified template (genomic DNA) should be handled. The
digestion and ligation reactions should be conducted in this area. The
PCR reactions should be prepared in this area. The use of gowns,
booties, and gloves is recommended to prevent PCR carryover.
Each room should contain dedicated equipment such as
thermocyclers, microfuges, pipets, tips, etc.