Array Advice - Sample Quality

View tips and solutions to common problems for array sample quality.

Tips

  • Ensure gDNA has 260/280 between 1.8 and 2.0, and 260/230 greater than 1.5 before proceeding to microarray analysis.

Solutions to Common Problems

Problem 1 - Poor quality DNA as seen from 260/280 and 260/230 ratios

Cause: Impurities in the DNA.

  • High A260/A280 (>2.0) indicates RNA contamination.
  • Low A260/A280 (<1.8) indicates protein contamination.
  • Low A260/A230 (<1.5) indicates contamination of salts or solvents (e.g. Phenol).

Solution: 

  • High A260/A280 - ensure RNase is used during DNA extraction.
  • Low A260/A280 - ensure proteinase K is used during DNA extraction; gDNA can also be purified.
  • Low A260/A230 - re-purify by ethanol precipitation.

 

Problem 2 - High DLR

Cause: Poor DNA quality. 

Solution: Check the DNA quality on an agarose gel for degradation (see figure 1 below). If a smear is observed on the gel, re-extract the sample.

Fig 1. Examples of DNA quality

Figure 1. Examples of DNA quality

 

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