What's Wrong with My Arrays?

• Re-purify samples using proteinase steps

• Ensure that your DNA extraction protocol includes RNase

• Re-purified by ethanol precipitation
• Resuspending the DNA in TE buffer

• Dilute DNA 1:2 in water or suitable buffer

The wrong temperatures or times are being used

• Check temperatures with a calibrated thermometer
• Check incubation times against protocol

Incorrect volumes used in mastermix preparation

• Check correct volumes are being added
• Check pipettes are calibrated correctly

Insufficient mixing of samples, reagents and mastermixes

• Gently vortex all reagent tubes (except Klenow)
• Flick mix Klenow tube
• Briefly spin to drive contents off tube walls

Too much exposure to light or air

• Use a closed thermal cycler with heated lid

Loss of solution from evaporation

• Use PCR machine with a heated lid
• If using tubes, make sure lids are tightly closed
• If using plates, use caps not a plate sealer

• Ensure the correct volume of hybridisation solution has been used
• Check no leakage of hybridisation solution has occurred

• Check the backing slide seal is intact and has not cracked
• Report any gasket slide failures to our support team

• Check oven rotators are working
• Remove jigs from oven one at a time
• Disassemble under wash buffer rapidly

• Ensure dishes are regularly cleaned with appropriate solvent
• Ensure clean gloves, forceps and dishes
• Carry out additional acetonitrile wash for 1 minute at room temperature

• Ensure dishes are regularly cleaned with appropriate solvent
• Ensure clean gloves and forceps
• Check stirrer is producing a vortex prior to adding slides in wash buffer
• Check temperature of oven and washes

• Check protocol for correct wash instructions
• Cover tubes with foil or use amber tubes
• Check temperature of oven and washes

• Ensure slides are scanned immediately after washing
• Enclose scanners in a box with ozone scrubbers

• Ensure slides are scanned immediately after washing
• Enclose scanners in a box with ozone scrubbers