Mapping 250K/500K SNP assay

chapter 8 | Troubleshooting 213
10. For the 96-well plate protocol, we highly recommend all
mutlichannel pipettes be calibrated regularly.
11. For the 96-well plate protocol, we recommend using a team
approach to sample processing for greater efficiency. This approach
is described on page 37.
Important Differences Between GeneChip ® Mapping
Arrays and GeneChip ® Expression Arrays
12. For laboratories that also run GeneChip Expression arrays it is
important to check the temperature setting on the Hybridization
Oven 640. For the GeneChip ® Mapping 250K Nsp Array and the
GeneChip ® Mapping 250K Sty Array, ovens should be set to
49°C. The temperature for hybridization on expression arrays is
45°C.
We also recommend that your hybridization ovens be serviced at
least once per year to ensure that they are operating within
manufacture specifications
13. Buffer B is different for the expression and DNA arrays. Using the
MES based buffer B from the Expression protocol will result in
substantially reduced call rates for the GeneChip ® Mapping 500K
Set. Also, care should be taken to ensure the fluidics station is
properly maintained and primed with the correct buffers prior to
use.
14. Both the GeneChip Mapping 500K and Expression protocols use
the same stain reagents for each staining step. However, after the
last wash the Mapping 250K Array is filled with Array Holding
Buffer.
15. The arrays in the GeneChip ® Mapping 500K Set are scanned once
at 570 nm on the GeneChip ® Scanner 3000 7G.