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