Array Advice - General
View solutions to common problems for arrays:
Solutions to common problems
Problem 1: Low/no signal on array
- Poor DNA labelling
- Wrong side of the slide was hybridised
- Wrong side of the slide was scanned
- Check labelling efficiency on a Nanodrop
- Ensure correct side of slide was hybridised
- Check that the correct side of the slide was scanned
Problem 2 – Poor signal intensity
Figure 1. Example of poor signal intensity
- Poor DNA quality or low input
- Errors during the labelling reaction e.g. pipetting, purification step
- Wash or hybridisation conditions too stringent
- Cy5-labeled targets were exposed to light
- Re-quantify or purify gDNA.
- Ensure protocol is followed.
- Hybridisation oven temp should not be greater than 67˚C and slides should be in wash buffer 2 for no more than 1 minute.
- Cover tubes with aluminium foil or use amber microcentrifuge tubes.
Problem 3 – Poor SNP data
Figure 2. Examples of good and poor SNP data
Possible cause: Hybridisation oven/wash buffer 2 temperature incorrect
- Ensure oven temp is between 65-67˚C by using a calibrated thermometer that is attached to the rotator to mimic temp of the array
- Buffer 2 taken out too early from 37˚C incubator
- Ensure that the wash area and the 37˚C incubator are close to each other so that the wash buffer 2 temp does not drop too low during transport.
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