Matt:LabNotes/2017-6-19: Difference between revisions

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'''Program'''<br>
'''Program'''<br>
*95C 30sec -> cool down to 55 C at 0.02C/sec -> 55 C 16h
*95C 30sec -> cool down to 55 C at 0.02C/sec -> 55 C 16h
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**Should have added RiboLock after reached 55C since it would be denatured at 95C
*Ampligase: add 3ul AmpLigase enzyme mix (0.5U/ul AmpLigase in 1X AmpLigase buffer)
*Ampligase: add 3ul AmpLigase enzyme mix (0.5U/ul AmpLigase in 1X AmpLigase buffer)
*SplintR: add 3ul SplintR enzyme mix (13.5ul SplintR + 2.25ul 10X SplintR Buffer + 6.75ul H2O)
*SplintR: add 3ul SplintR enzyme mix (10ul SplintR + 2ul 10X SplintR Buffer + 4ul Ribolock + 4ul H2O)
*Ampligase: -> 55 C 20h -> 94C 2min -> add 2ul Exo I/III mix -> 37C 1h -> 94C 2min -> 4C hold
*Ampligase: -> 55 C 20h -> 94C 2min -> add 2ul Exo I/III mix -> 37C 1h -> 94C 2min -> 4C hold
*SplintR: -> 37 C 15min -> 94C 10min -> add 2ul Exo I/III mix -> 37C 1h -> 94C 2 min -> 4C hold
*SplintR: -> 37 C 30min -> 94C 10min -> add 2ul Exo I/III mix -> 37C 1h -> 94C 2 min -> 4C hold
*Zymo columns
*Zymo columns
**Elute 10ul
**Elute 10ul
**Sample 2 was only able to pipette 20ul instead of 30ul of the ligation reaction so theoretically has 33% lower conc after elution from column
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====AmpLigase enzyme mix====
====AmpLigase enzyme mix====

Revision as of 18:56, 20 June 2017

Agi15k_Feb2017 V4 + 5% formamide in vitro Capture

Calculate Probes Needed

V4

Probe:target 1000:1 '
Probe size 4998 probes
DNA templet 300 ng
gDNA MW 1.95x10^12 g/mol
gDNA (300ng) 1.5385x10^-19 mol
Probe (1000:1) 1.5385x10^-16 mol
Probe MW (4998, 157nt) 2.387x10^8 g/mol
Amount Probe req'd 36.7 ng


Probes, Target and Ampligase Buffer Mix

Sample Condition V4 (10.3ng/ul) 12878 DNA (80.3ng/ul) UHRR (1ug/ul) Ampligase Buffer SplintR Buffer Formamide or DMF Ribolock 40U/ul H2O Total
1 Ampligase DNA 3.6 3.8 0 3 0 0 0 19.6 30
2 Ampligase NTC 3.6 0 0 3 0 0 0 23.4 30
3 SplintR 10% DMF DNA 3.6 3.8 0 0 3 3 0 16.6 30
4 SplintR 10% DMF RNA 3.6 0 1 0 3 3 0.5 18.9 30
5 SplintR 10% DMF NTC 3.6 0 0 0 3 3 0 20.4 30
6 SplintR 5% formamide DNA 3.6 3.8 0 0 3 1.5 0 18.1 30
7 SplintR 5% formamide RNA 3.6 0 1 0 3 1.5 0.5 20.4 30
8 SplintR 5% formamide NTC 3.6 0 0 0 3 1.5 0 21.9 30

Program

  • 95C 30sec -> cool down to 55 C at 0.02C/sec -> 55 C 16h
    • Should have added RiboLock after reached 55C since it would be denatured at 95C
  • Ampligase: add 3ul AmpLigase enzyme mix (0.5U/ul AmpLigase in 1X AmpLigase buffer)
  • SplintR: add 3ul SplintR enzyme mix (10ul SplintR + 2ul 10X SplintR Buffer + 4ul Ribolock + 4ul H2O)
  • Ampligase: -> 55 C 20h -> 94C 2min -> add 2ul Exo I/III mix -> 37C 1h -> 94C 2min -> 4C hold
  • SplintR: -> 37 C 30min -> 94C 10min -> add 2ul Exo I/III mix -> 37C 1h -> 94C 2 min -> 4C hold
  • Zymo columns
    • Elute 10ul