Matt:LabNotes/2017-6-6: Difference between revisions

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>Mzcai
(Created page with "==Agi15k_Feb2017_V4 Probe Production== *Production of Padlock Probes (V4) Matt:LabNotes/2017-2-8 ===Production PCR=== *Matt:LabNotes/2017-3-30 | 25nM 1st round amplicon...")
 
>Mzcai
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*Purified 8 tubes of 100ul in 8 columns following Qiagen protocol
*Purified 8 tubes of 100ul in 8 columns following Qiagen protocol
*Eluted each column with 50ul and combined all into one 1.5ml
*Eluted each column with 50ul and combined all into one 1.5ml
*Measured concentration with Nanodrop:<!--
*Measured concentration with Nanodrop:
~400ul of V4 probes: 244.2 ng/ul => ~97.64 ug
~400ul of V4 probes: 248.3 ng/ul => ~99.3 ug


===Lambda Exonuclease Digestion===
===Lambda Exonuclease Digestion===
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*Purified with 8 Zymo ssDNA/RNA columns
*Purified with 8 Zymo ssDNA/RNA columns
*Eluted with 40ul each
*Eluted with 40ul each
*Recombined and measured ssDNA with Nanodrop:
*Recombined and measured ssDNA with Nanodrop:<!--
**2hr incubation: 81.7 ng/ul x 160ul =  13 ug
**2hr incubation: 81.7 ng/ul x 160ul =  13 ug



Revision as of 19:50, 7 June 2017

Agi15k_Feb2017_V4 Probe Production

Production PCR

Components Volume (1X) Volume (100X)
First round amplicon Agi15k_Feb2017_V4 (25nM) 0.1 10
2X KAPA SYBG MM 50 5000
AP1V4U (100uM) 0.4 40
AP2V4 (100uM) 0.4 40
H2O 49 4910
Total 100 10000

Program 98C 1min -> (98C 10sec -> 55C 30sec -> 72C 45sec) x 13 -> 72C 2min -> 15C hold

EtOH Precipitation

  • 8 5-ml tubes (with 12 wells of PCR product each) for V4
    • 1200ul PCR product
    • 3000ul 100% EtOH
    • 3ul GlycoBlue
    • 120ul 3M NaOAc pH 5.2-5.5
  • Vortexed and put in -80C for overnight
  • Centrifuged at 3,000rpm at 4C for 30 min
  • Discarded supernatant and added 800ul of cold 80% EtOH
  • Transferred DNA pellet (with 1ml pipette tip) to 8 1.5mL tubes
  • Centrifuged 1.5ml tubes at 14,000rpm for 5 min at 4C
  • Discarded supernatant and air-dried for 10 min in hood
  • Resuspended DNA with 100ul H2O

Qia Column Purification

  • Purified 8 tubes of 100ul in 8 columns following Qiagen protocol
  • Eluted each column with 50ul and combined all into one 1.5ml
  • Measured concentration with Nanodrop:

~400ul of V4 probes: 248.3 ng/ul => ~99.3 ug

Lambda Exonuclease Digestion

  • Divide into 4 pcr tubes of ~100ul with total amplicon of <10ug each
Components Volume
Amplicon 96
10X Lambda Exo Buffer 12
Lambda Exonuclease 12
Total 120
  • Incubate 4 tubes at 37C for 2hr
  • Purified with 8 Zymo ssDNA/RNA columns
  • Eluted with 40ul each
  • Recombined and measured ssDNA with Nanodrop: