User:Tara K. Luckau/Notebook/Team ConGen/2011/10/14: Difference between revisions
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====Best conditions==== | ====Best conditions==== | ||
* Scun7_25_SYRa | * Scun7_25_SYRa | ||
: Scun7 - 0.25 µL | :: <span style="color:#FFFFFF; background:#4169E1">Scun7 - 0.25 µL</span> | ||
: Scun10 - 0.15 µL | :: Scun10 - 0.15 µL | ||
: Scun16 - 0.2 µL | :: Scun16 - 0.2 µL | ||
: Scun22 - 0.2 µL | :: Scun22 - 0.2 µL | ||
: [[Image:20111014 Frag3.png|700 px]] | : [[Image:20111014 Frag3.png|700 px]] | ||
* Scun16_15_SYRa | * Scun16_15_SYRa | ||
: Scun7 - 0.2 µL | :: Scun7 - 0.2 µL | ||
: Scun10 - 0.15 µL | :: Scun10 - 0.15 µL | ||
: Scun16 - 0.15 µL | :: <span style="color:#FFFFFF; background:#4169E1">Scun16 - 0.15 µL</span> | ||
: Scun22 - 0.2 µL | :: Scun22 - 0.2 µL | ||
: [[Image:20111014 Frag4.png|700 px]] | : [[Image:20111014 Frag4.png|700 px]] | ||
* Scun19_30_SYRb | |||
: Scun9 - 0.3µL | |||
: Scun15 - 0.25 µL | * Scun19_30_SYRb (but Scun19 usually did not amplify to detectable levels) | ||
: Scun19 - 0. | :: Scun9 - 0.3µL | ||
:: Scun15 - 0.25 µL | |||
:: <span style="color:#FFFFFF; background:#006400">Scun19 - 0.3 µL</span> | |||
: [[Image:20111014 Frag5.png|700 px]] | : [[Image:20111014 Frag5.png|700 px]] | ||
==Multiplexing and AutoDimer== | |||
* Looked into whether there are tools available to check interactions between primers when multiplexing | |||
* Found AutoDimer by NIST (Butler 2004) | |||
:: http://yellow.nist.gov:8444/dnaAnalysis/primerToolsPage.do | |||
* Ran SCOC primers, within each color lane, just out of curiosity | |||
:*Only got one interaction at default settings (in the blue lane): | |||
:: [[Image:20111014 Primer.png|700 px]] | |||
:* When threshold was decreased to 4, more interactions: | |||
:: [[Image:20111014 Primer2.png|700 px]] | |||
* I think it's useful to decrease the threshold to 4 or 5 to have program spit out more interactions, and be able to decide for myself which ones I care about | |||
==Next Steps== | |||
* optimize within yellow lane (Scun3, Scun11, sar80) | |||
* see if green and yellow can multiplex (same PCR conditions) | |||
* diversity panel on all lanes, and post-PCR mix | |||
Revision as of 15:53, 17 October 2011
Tara's Lab Notebook | <html><img src="/images/9/94/Report.png" border="0" /></html> Main project page <html><img src="/images/c/c3/Resultset_previous.png" border="0" /></html>Previous entry<html> </html>Next entry<html><img src="/images/5/5c/Resultset_next.png" border="0" /></html> |
SCOC MP1Fragment AnalysisSummary of fragment analysis results
Best conditions
Multiplexing and AutoDimer
Next Steps
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