Daniel:Notebook/HiResChrPaint/2014-7-10

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Probe Mining-Stellaris[edit]

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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