Matt:LabNotes/2015-6-29: Difference between revisions

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>Mzcai
(Created page with "==CA12k_Nov2014_V4 Probe Production== *Production of Padlock Probes (V4) Matt:LabNotes/2014-11-19#Assembly_of_oligo_pool_for_ordering *Train Justin ===Production PCR=== *...")
 
>Mzcai
mNo edit summary
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**80ul 3M NaOAc pH 5.2-5.5
**80ul 3M NaOAc pH 5.2-5.5


*Vortexed and put in -80C for overnight<!--
*Vortexed and put in -80C for overnight
*Centrifuged at 3000rpm at 4C for 30 min
*Centrifuged at 3000rpm at 4C for 30 min
*Discarded supernatant and added 800ul of cold 80% EtOH
*Discarded supernatant and added 800ul of cold 80% EtOH
Line 49: Line 49:
*Measured concentration with Nanodrop:
*Measured concentration with Nanodrop:


~575ul of V4 probes: 86.9 ng/ul => ~50 ug
~585ul of V4 probes: 77.0 ng/ul => ~45 ug


===Lambda Exonuclease Digestion===
===Lambda Exonuclease Digestion===
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*Incubated at 37C for 1hr
*Incubated at 37C for 1hr
*Purified with 6 Zymo ssDNA/RNA columns
*Purified with 6 QIA columns
*Eluted with 40ul each
*Eluted with 40ul each
*Recombined and measured ssDNA with Nanodrop:
*Recombined and measured ssDNA with Nanodrop:
**79.2ng/ul x 240ul = 19ug (76% yield)
**42.8ng/ul x 240ul = 10.3ug (46% yield)


===Remove Amplification Adapters===
===Remove Amplification Adapters===
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*Added 5ul DpnII
*Added 5ul DpnII
*Incubated at 37C for overnight (~15hrs)
*Incubated at 37C for overnight (~15hrs)
 
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===Zymo Column Purification===
===Zymo Column Purification===
*Eluted 30ul each column (115ul total)
*Eluted 30ul each column (115ul total)

Revision as of 21:40, 30 June 2015

CA12k_Nov2014_V4 Probe Production

Production PCR

Components Volume (1X) Volume (100X)
First round amplicon CA12k_Nov14_V7 (10nM) 0.2 20
2X KAPA SYBG MM 50 5000
AP1V4U (100uM) 0.4 40
AP2V4 (100uM) 0.4 40
H2O 49 4900
Total 100 10000
  • 2 wells were spilled so left empty

Program 98C 1min -> (98C 10sec -> 55C 30sec -> 72C 45sec) x 15 -> 72C 2min -> 15C hold File:20150629 CA12kNov14 ProductionPCR V4.JPG

EtOH Precipitation

  • 12 5-ml tubes (with 8 wells of PCR product each) for V4
    • 800ul PCR product
    • 2000ul 100% EtOH
    • 2.7ul GlycoBlue
    • 80ul 3M NaOAc pH 5.2-5.5
  • Vortexed and put in -80C for overnight
  • Centrifuged at 3000rpm at 4C for 30 min
  • Discarded supernatant and added 800ul of cold 80% EtOH
  • Transferred DNA pellet (with 1ml pipette tip) to 6 1.5mL tubes
  • Centrifuged 1.5ml tubes at 14,000rpm for 5 min at 4C
  • Discarded supernatant and air-dried for 5 min in hood
  • Resuspended DNA with 100ul H2O

Qia Column Purification

  • Purified 12 tubes of 100ul in 12 columns following Qiagen protocol
  • Eluted each column with 50ul and combined all into one 1.5ml
  • Measured concentration with Nanodrop:

~585ul of V4 probes: 77.0 ng/ul => ~45 ug

Lambda Exonuclease Digestion

  • Divide into 6 pcr tubes of ~100ul with total amplicon of <10ug each
Components Volume
Amplicon 96
10X Lambda Exo Buffer 12
Lambda Exonuclease 12
Total 120
  • Incubated at 37C for 1hr
  • Purified with 6 QIA columns
  • Eluted with 40ul each
  • Recombined and measured ssDNA with Nanodrop:
    • 42.8ng/ul x 240ul = 10.3ug (46% yield)

Remove Amplification Adapters

USER

  • Split into 4 PCR tubes and add 5ul USER
Components Volume
SS-amplicon 59
USER 5
10X DpnII Buffer 8
H2O 8
Total 80
  • Incubate at 37C for 2.5 hours

DpnII

  • Added 15ul of the following
Components Volume
10X DpnII Buffer 2
100uM RE-DpnII_V4 guide oligo 5
H2O 8
  • Incubated at 94C for 2 min, then 37C for 3 min
  • Added 5ul DpnII
  • Incubated at 37C for overnight (~15hrs)