Mapping 250K/500K SNP assay

218 GeneChip ® Mapping 500K Assay Manual
OD Troubleshooting Guidelines
Refer to the tables below when troubleshooting OD readings.
Table 8.1
PROBLEM: Average Sample OD is greater than 0.7 (3.5 µg/µL)
If the average sample OD of three independent measurements is greater than 0.7 (calculated concentration
greater than 3.5 µg/µL), a problem exists with either the elution of PCR products or the OD reading. The
limit on PCR yield is approximately 3.5 µg/µL, as observed in practice and as predicted by the mass of
dNTPs in the reaction.
Possible causes include:
The purified PCR product was eluted in a volume less than 45 µL.
The purified PCR product was not mixed adequately before making the 1:100 dilution.
The diluted PCR product was not mixed adequately before taking the OD reading.
The water blank reading was not subtracted from each sample OD reading.
The spectrophotometer plate reader may require calibration.
Pipettes may require calibration.
There may be air bubbles or dust in the OD plate.
There may be defects in the plastic of the plate.
The settings on the spectrophotometer plate reader or the software may be incorrect.
OD calculations may be incorrect and should be checked.
Reliance on any single OD reading may give an outlier result. You should make three independent dilutions
and take three independent OD readings per dilution.