Overnight 16 Hour Gel
To test how intact the DNA is from the recent Hirt and puregene of virus DNA from infected Dinn cells, I wanted to run an overnight gel as I have done previously.
We had also purchased a special agarose that is for pluse-phase gels or HMW gels: seakem lonza gold agarose, which I wanted to try if this resolves the bands better.
For this gel I ran: 3 Hirt cell samples, 2 hirt supernatant samples, and both puregene samples.
I used 10ul of each sample, with 2ul of loading dye
- 0.7% gel mix:
- 160mL 1X TAE
- 1.155g agarose
- Microwaved for ~4min
- Added 2ul midori stain
- Pipetted 1mL into a 1.5mL tube and saved on the heat block at 65 degrees C make sure the heat block is on and running
- Made sure the large tray had well sealed tape barriers
- Let the gel liquid cool for ~10 min until pouring into the tray and placing in the combs
- Gel cooled in ~20 min or less
- Added 1 round of PFG ladder to the left-most well
- Let the 1mL saved gel cool for ~3 min outside of the heat block
- Filled the PFG well with cooled gel liquid to the top of the well to seal the round in
- Waited ~3 minutes for the wells to cool
- Made up 48kb ladder:
- 6ul ladder
- 30ul loading dye
- 144ul molecular grade water
- Placed the gel tray into the box after removing the tape
- Mixed samples with loading dye in strip tubes
- Added 5ul 48kb ladder to 2 wells in the gel (I should have used more of this)
- Added in the 12ul of each sample
- Set the timer for 16.5 hours at 40 volts and started it at ~5:14pm
- Gel was stopped at ~9:15am
