Daniel:Notebook/RNAFISH/2014-7-7: Difference between revisions
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##VI command, forward: :%s!^!GTCATATCGGTCACTGTT! | ##VI command, forward: :%s!^!GTCATATCGGTCACTGTT! | ||
##VI command, reverse: :g/$/norm AGATCAGGATACACACTACCC | ##VI command, reverse: :g/$/norm AGATCAGGATACACACTACCC | ||
##Primer sequences are AP1 and AP2 from the V6 set, used in High Resolution Chromosome Painting |
Revision as of 21:49, 7 July 2014
Probe Design
Designing probes for Matt and Hosuk's rolony project. The three genes they are testing are ACTB, RAB7A, and MALAT1. I will design probe sets for these three genes.
Workflow
- Obtain transcript sequence from Genome Browser
- Use genome browser to find genes, and tables to download transcript (mRNA only)
- Use gene sequence as input for probe designer
- Designer created by Arjun Raj, utilized by Long Cai for paper
- Creates 20mer probes
- Copy/paste probe sequences into .txt file
- Print only sequence to the oligo file
- awk '{print $2}' malat1_probes.txt > oligos_malat1.txt
- Attach primer sequences before/after
- VI command, forward: :%s!^!GTCATATCGGTCACTGTT!
- VI command, reverse: :g/$/norm AGATCAGGATACACACTACCC
- Primer sequences are AP1 and AP2 from the V6 set, used in High Resolution Chromosome Painting