Phenol Chloroform Extraction Test using AMKE feathers (All body feathers)
- Update: We were able to get bands on the 1% agarose gel, using 3 μL of DNA sample. The goal is to find the best clean up method for post extraction to clean up the smeared (degraded) DNA.
- First Bead Clean Up using a 1:1 ratio of Ampure XP beads:
 
- Second Bead Clean Up using a .5X beads on 4 of the samples from above that already went through the 1st Bead Clean Up:
 
- 22Aug2017: The next objective would be to try different ratios of Ampure Beads on a sheared AMKE sample, .5X and .4X but with only a 1 minute incubation. Rep from Beckman Coulter says that the first thing to bind to beads are the largest fragments, longer incubation will mean more time for smaller fragments to bind to beads. She recommended Ampure XP vs SPRI for genomic DNA, with a left side selection. Also recommended a longer elution incubation (10 min.). Larger fragments stick onto beads more and need more time to come off. If we had a 37 degrees water bath, we can incubate in there for just 5 min. Beckman contact: Nina at extension 358445 press * key after dialing 1-800-369-0333.
- 24Aug2017: Performed Ampure XP bead clean up with a sheared AMKE sample to mimic degraded DNA (used Bioruptor). Tested 4 different ratios of beads on 100 μL samples. The best ratio is 100 μL sample to 40 μL beads (0.40X):
 
- Bead Clean Up, incubation time 2 minutes. Need to redo clean up with shorter incubation to get rid of small fragments:
 
- 30Aug2017: Second Bead clean up, shorter incubation and quicker removal of supernatant:
 
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