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

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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|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).
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===
===Workflow===
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#Obtained CDS region of dystrophin gene using UCSC genome browser
#Obtained CDS region of dystrophin gene using UCSC genome browser
#Took first 8000bp (Stellaris maximum) and generated a 32bp probe set
#Took first 8000bp (Stellaris maximum) and generated a 32bp probe set
##[[Media:Dystrophin_probes.txt‎|Probe list]], columns: probe# sequence startpos GCcontent
##[[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