Array Advice - Sample Quality
View tips and solutions to common problems for array sample quality.
- 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).
- 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.
Figure 1. Examples of DNA quality
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