CTR:Notebook/PIRE/2015/04/01

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RAD Library Prep - Skinks Plate 2

  • 96 well plate of 50ng of DNA 10uL
  • Digestion (2015-03-31)
    • Mix and add to each well:
      • 0.68 uL water
      • 1.20 uL NEBuffer 4
      • 0.12 uL SbfI-HF
    • Incubation (RADIGEST on TONY):
      • 37 degrees for 60 minutes
      • 65 degrees for 20 minutes
  • P1 adapter ligation (2015-03-31)
    • Add 2 uL indexed P1 adapter (10nM) to each well, using new plate of adapters made in-house
    • Mix and add to each well:
      • 1.28 uL water
      • 0.40 uL NEBuffer 4
      • 0.16 uL ATP
      • 0.16 uL T4 Ligase
    • Incubation (RADLIG on TONY):
      • 20 degrees for 60 minutes
      • 65 degrees for 20 minutes
  • Clean up (2015-04-01)
    • Take 5 uL from each well and combine to 1.7 mL tube
    • AMPure bead clean up:
      • Used 460 uL beads to DNA (1:1)
      • 2 washes of 800 uL 80% EtOH
      • Elute in 100 uL LowTE
  • Sonication (2015-04-01)
    • BioRuptor NGS: 8 cycles of 15 seconds on, 90 seconds off, High Power

1) 2uL 100bp low scale ladder, 2) 2uL sheared DNA
Additional 6 cycles of 15 seconds on, 90 seconds off, High Power
1) 2uL 100bp low scale ladder, 2) 2uL sheared DNA

  • Blunt End Repair (2015-04-02)
    • Mix:
      • 50.0 uL fragmented DNA
      • 5.5 uL water
      • 3.0 uL End Prep Enzyme Mix
      • 6.5 uL End Repair Reaction Buffer
    • Incubation (NEBENDRP on JOHN Block B):
      • 20 degrees for 30 minutes
      • 65 degrees for 30 minutes
  • P2 adapter ligation (2015-04-02)
    • Add to mix:
      • 15.0 uL Blunt/TA Ligase Master Mix
      • 2.5 uL P2 RAD adapter (5 uM)
      • 1.0 uL Ligation Enhancer
    • Incubation (NEBLIGAT on JOHN Block B):
      • 20 degrees for 15 minutes
  • Size selection (2015-04-02)
    • Add 16.5 uL water for a total of 100 uL
    • AMPure bead size selection:
      • 45 uL beads to remove large fragments
      • 25 uL beads to remove small fragments
      • 3 washes of 200 uL 80% EtOH
      • Elute in 20 uL LowTE
  • PCR amplification (2015-04-02)
    • Mix:
      • 5 uL DNA
      • 25 uL NEBNext High Fidelity 2x PCR Master Mix
      • 18 uL water
      • 1 uL P1 adapter primer (25 uM)
      • 1 uL P2 adapter primer (25 uM)
    • PCR cycle (NEBPCR on JOHN Block B):
      • 98 degrees for 30 seconds
      • 15 cycles of:
        • 98 degrees for 10 seconds
        • 65 degrees for 30 seconds
        • 72 degrees for 30 seconds
      • 72 degrees for 5 minutes

1) 1 uL DNA template, 2) 5 uL PCR product, 3) 2 μL 100bp ladder

  • Re-run PCR (2015-04-03)
    • Mix:
      • 10 uL DNA
      • 25 uL NEBNext High Fidelity 2x PCR Master Mix
      • 13 uL water
      • 1 uL P1 adapter primer (25 uM)
      • 1 uL P2 adapter primer (25 uM)
    • PCR cycle (NEBPCR on JOHN Block B)

1) 5 uL PCR product, 2) 1 μL template, 3) 2 μL 100bp ladder

  • Qubit: 5.98 ng/μL


  • Run 3μL on BioAnalyzer DNA High Sensitivity Chip (2015-02-06)

RAD Library Re-prep - Skinks Plate 2

Reprep from plate.

  • Digestion (2015-04-29)
    • RADIGEST on TONY
  • P1 adapter ligation (2015-04-29)
    • Used new plate of adapters made in-house
    • RADLIG on TONY
  • Clean up (2015-04-30)
    • Used 432μL Serapure beads to DNA (1:1)
  • Sonication (2015-04-30)
    • BioRuptor NGS: 8 cycles of 15 seconds on, 90 seconds off, High Power


1) 2uL sheared DNA, 2) 2uL 100bp low scale ladder

  • Blunt End Repair (2015-04-30)
    • New NEBNext kit reagents used
    • NEBENDRP on JOHN Block A
  • P2 adapter ligation (2015-04-30)
    • New NEBNext kit reagents used
    • NEBLIGAT on JOHN Block A
  • Size selection (2015-04-30)
    • AMPure bead size selection:
      • 45 uL beads to remove large fragments
      • 25 uL beads to remove small fragments
  • PCR amplification (2015-04-30)
    • NEBPCR on JOHN Block A


1) 2uL 100bp low scale ladder, 2) 5uL of PCR product, 3) 1uL of template

  • Qubit: 8.74 ng/uL
  • 2nd PCR amplification (2015-05-01)
    • Used 10 uL of template
    • NEBPCR on JOHN Block A


1) 2uL 100bp low scale ladder, 2) 5uL of PCR product

  • Bead clean up
    • Use 45 uL AMPure beads (1:1)
    • 2 washes of 200 uL 80% EtOH
    • Elute in 30 uL LowTE
  • Picogreen: 5.43 ng/uL
  • Qubit: 9.82 ng/uL
  • Ran 3μL on BioAnalyzer DNA High Sensitivity Chip (2015-02-06)



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