Mapping 250K/500K SNP assay

Table 4.24
PROBLEM: Average Sample OD is Less Than 0.5 (2.5 µg/µL)
chapter 4 | 96-Well Plate Protocol 93
Troubleshooting Possible Problems with the Elution or OD Readings – possible causes include:
The purified PCR product was eluted in a volume greater 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.
Table 4.25
PROBLEM: OD260/OD280 ratio is not between 1.8 and 2.0
Possible causes include:
The PCR product may be not be sufficiently purified. Be sure to perform three water washes and check
to be sure the vacuum manifold is working properly.
An error may have been made while taking the OD readings.