1.8X Bead clean of oyster DNA samples post sonication

DNA samples were previously sonicated down to a modal size of 150 bp, documented here. Before moving on to library prep, I performed a 1.8X bead clean to concentrate the 500 ng of DNA in 25 uL of 10 mM Tris HCl pH 8.

Completed April 27 and 28, 2021

• Performed the bead clean on 8 or 9 samples at a time:
  • 1st round: NAR_8, NAR_9, GHP_6, BAR_2, BAR_8, KIC_4, KIC_8, MCD_5
  • 2nd round: NAR_4, NAR_10, GHP_1, GHP_3, GHP_5, GHP_10, BAR_3, BAR_6
  • 3rd round: NAR_1, NAR_3, BAR_9, KIC_7, KIC_9, MCD_1, MCD_2, MCD_7
  • 4th round: NAR_6, GHP_8, GHP_4, BAR_1, BAR_4, BAR_10, KIC_2, KIC_5
  • 5th round: NAR_2, NAR_5, NAR_7, GHP_2, GHP_7, KIC_6, MCD_4, MCD_6, MCD_9
  • 6th round: GHP_9, BAR_5, BAR_7, KIC_1, KIC_3, KIC_10, MCD_3, MCD_8, MCD_10

1.8X Bead clean

• Make fresh 80% EtOH
• Take KAPA Pure beads out of fridge to warm to room temperature for ~30 minutes
• Take DNA samples out of freezer and let thaw
• Vortex and spin down samples
• Add 90 uL of KAPA Pure beads to each sample
  • Pipette up and down 10 times to mix
• Incubate at room temperature for 15 minutes on shaker
• Place tubes on magnet rack and remove supernatant when clear (~138 uL)
• Add 200 uL of 80% EtOH to each tube while still on magnet without disturbing the beads
• Remove 197 uL of clear supernatant
• Add 190 uL of 80% EtOH to each tube while still on magnet without disturbing the beads
• Remove ALL of clear supernatant
  • Use a pipette tip to remove any droplets inside tubes
• Resuspend beads in 25 uL of 10 mM Tris HCl pH 8
• Incubate at room temperature for 5 minutes on shaker
• Make new set of labeled PCR-strip tubes for each sample
• Place tubes on magnet, transfer clear supernatant to appropriate PCR strip tube

Qubit dsDNA Broad Range assay

Checked the quantification of two samples following Qubit protocol for BR DNA