Matt:LabNotes/2013-7-1: Difference between revisions

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   Program
   Program
   *98°C 30sec -> (98°C 10sec -> 52°C 30sec -> 72°C 30sec) x8 cycles -> (98°C 10sec -> 72°C 30sec) x7 cycles -> 72°C 3 min -> 15°C hold
   *98°C 30sec -> (98°C 10sec -> 52°C 30sec -> 72°C 30sec) x8 cycles -> (98°C 10sec -> 72°C 30sec) x7 cycles -> 72°C 3 min -> 15°C hold
[[File:07012013_Agi26kCapturedSequencePCRGraph.JPG | 650px]]
*Sample with greatest amplification is NTC for 20gap probes
**Will run a gel to see what is causing the signal
*Both 20gap samples did not show amplification suggesting something went wrong
**Possibly the dNTP mix used during capture reaction is to blame because Noi says the Stoffel fragment enzyme was working a week ago
*Both 0gap samples showed moderate amplification and NTC was as expected

Revision as of 21:46, 1 July 2013

Continued from: http://genome-tech.ucsd.edu/LabNotes/index.php/Matt:LabNotes/2013-6-28

Amplification with Sequencing Adapters

  • Since this is the same design as LC Sciences probes that Noi used, I'll use the same primers
Tube # Sample Index#
1 NTC-0gap Indx7
2 gDNA-0gap Indx45
3 cDNA-0gap Indx76
4 NTC-20gap Indx7
5 gDNA-20gap Indx77
6 cDNA-20gap Indx78


Will also do duplicate for each sample so 12 reactions total

Components 1 rxn 13 rxn
Captured template 12.00 0.00
10uM Forward+Indx 2.00 0.00
10uM Reverse 2.00 26.00
2x KAPA SYBG fast MM 50.00 650.00
H2O 34.00 442.00
Total 100.00 1300.00
 Program
 *98°C 30sec -> (98°C 10sec -> 52°C 30sec -> 72°C 30sec) x8 cycles -> (98°C 10sec -> 72°C 30sec) x7 cycles -> 72°C 3 min -> 15°C hold

File:07012013 Agi26kCapturedSequencePCRGraph.JPG

  • Sample with greatest amplification is NTC for 20gap probes
    • Will run a gel to see what is causing the signal
  • Both 20gap samples did not show amplification suggesting something went wrong
    • Possibly the dNTP mix used during capture reaction is to blame because Noi says the Stoffel fragment enzyme was working a week ago
  • Both 0gap samples showed moderate amplification and NTC was as expected