Matt:LabNotes/2014-4-9: Difference between revisions

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>Mzcai
(Created page with "==Efficiency of Ampligase in situ Test== *Samples are wells F3-F10 from Matt:LabNotes/2014-3-31 ** # of Rolonies at each position *Ge...")
 
>Mzcai
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*Ligation with Ampligase should protect the padlock probes from digestion, hence comparing wells +Exo with those -Exo will show what percentage of padlock probes are ligated
*Ligation with Ampligase should protect the padlock probes from digestion, hence comparing wells +Exo with those -Exo will show what percentage of padlock probes are ligated


===Hybridize 1uM ppMALAT1===
===Hybridize 2uM ppMALAT1===
*Add 50ul 1uM ppMALAT1 for 20hr @45C in 1X Ampligase buffer +/- 0.5U/ul Ampligase
*Add 50ul 2uM ppMALAT1 for 20hr @45C in 1X Ampligase buffer +/- 0.5U/ul Ampligase


F3-F6: -Ampligase
F3-F6: -Ampligase
Line 17: Line 17:
| 10X Ampligase Buffer||20
| 10X Ampligase Buffer||20
|-
|-
| 100uM ppMALAT1||2
| 200uM ppMALAT1||2
|-
|-
| H2O||178
| H2O||178
Line 31: Line 31:
| 10X Ampligase Buffer||20
| 10X Ampligase Buffer||20
|-
|-
| 100uM ppMALAT1||2
| 200uM ppMALAT1||2
|-
|-
| 5 U/ul Ampligase||20
| 5 U/ul Ampligase||20

Revision as of 01:26, 10 April 2014

Efficiency of Ampligase in situ Test

  • General idea: Will use Exo I & Exo III OR Exo III only to digest non-ligased padlock probes, then use dcProbe2RevComp to hybridize to padlock probe and detect
    • Exo III only because it's possible Exo I will degrade all rolonies, leaving the padlock probe (even after ligation) nothing to attach to so it'll be washed away and not detected
  • Ligation with Ampligase should protect the padlock probes from digestion, hence comparing wells +Exo with those -Exo will show what percentage of padlock probes are ligated

Hybridize 2uM ppMALAT1

  • Add 50ul 2uM ppMALAT1 for 20hr @45C in 1X Ampligase buffer +/- 0.5U/ul Ampligase

F3-F6: -Ampligase

Component Volume
10X Ampligase Buffer 20
200uM ppMALAT1 2
H2O 178
Total 200

F7-F10: + Ampligase

Component Volume
10X Ampligase Buffer 20
200uM ppMALAT1 2
5 U/ul Ampligase 20
H2O 158
Total 200

Digestion

  • F3: Exo III
  • F4: Exo I/III
  • F5:
  • F6:
  • F7:
  • F8: Exo I/III
  • F9: Exo III
  • F10: