Just curious what everyone does. I'm trying to dispose of it responsibly, but it's tough to fill out the forms for hazardous waste pickup without knowing exactly what's in it. Do you have the waste picked up? How do you label it?
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For MiSeq waste I throw the cartridges away in biohazardous waste and usually dump PR2 down the sink with some water. The instrument waste should be treated as biohazardous and needs to be dumped accordingly.
For NextSeq waste there should be a wash protocol that rinses each well of the cartridge with a bleach solution. That way everything should be safe to toss in regular trash (except the instrument waste).
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For the MiSeq
We take the reagent cartridge to a fume hood after the run has finished, and use a thin plastic pipette to remove the solution from well position 8 that contains formamide. This goes into a bottle of formamide waste that is stored for proper disposal. After this the cartridge goes in the bin as we were told by Illumina the other wells do not contain any toxic reagents.
The wash and waste solutions go down the sink in the lab and are washed away with some water.
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