Daniel:Notebook/HiResChrPaint/2014-7-10: Difference between revisions

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>Djacobse
(Created page with "=Probe Mining-Stellaris= Back to Calendar Designing another set of probes for dystrophin. Some of the other probe designing software takes...")
 
>Djacobse
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[[Daniel:Notebook/HiResChrPaint|Back to Calendar]]
[[Daniel:Notebook/HiResChrPaint|Back to Calendar]]


Designing another set of probes for dystrophin.  Some of the other probe designing software takes a little while, but [https://www.biosearchtech.com/stellarisdesigner/|Stellaris] can generate a series of 20mer probes real quick.  So I'm using that to design a few probes  
Designing another set of probes for dystrophin.  Some of the other probe designing software takes a little while, but [www.biosearchtech.com|Stellaris] can generate a series of 20mer probes real quick.  So I'm using that to design a few probes for the dystrophin gene that can be detected quickly.  I'll be using a sparing amount for now, ordering 32 probes with an Amino modifier on the 5' end.  This will allow the probes to utilize the ARES technology, and I should be able to generate a FISH experiment with only dye labeling step followed by purification and FISH (no DpnII or Lambda exonuclease).
 
===Workflow===
 
#Obtained CDS region of dystrophin gene using UCSC genome browser
#Took first 8000bp (Stellaris maximum) and generated a 32bp probe set
##[[Media:Dystrophin_probes.txt‎|Probe list]]
##columns: probe# sequence startpos GCcontent


[[Category:HRCP]] [[Category:Probe Mining]] [[Category:Stellaris]]
[[Category:HRCP]] [[Category:Probe Mining]] [[Category:Stellaris]]

Latest revision as of 21:27, 10 July 2014

Probe Mining-Stellaris[edit]

Back to Calendar

Designing another set of probes for dystrophin. Some of the other probe designing software takes a little while, but [www.biosearchtech.com|Stellaris] can generate a series of 20mer probes real quick. So I'm using that to design a few probes for the dystrophin gene that can be detected quickly. I'll be using a sparing amount for now, ordering 32 probes with an Amino modifier on the 5' end. This will allow the probes to utilize the ARES technology, and I should be able to generate a FISH experiment with only dye labeling step followed by purification and FISH (no DpnII or Lambda exonuclease).

Workflow[edit]

  1. Obtained CDS region of dystrophin gene using UCSC genome browser
  2. Took first 8000bp (Stellaris maximum) and generated a 32bp probe set
    1. Probe list
    2. columns: probe# sequence startpos GCcontent