Daniel:Notebook/RNAFISH/2014-7-7

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Revision as of 21:49, 7 July 2014 by >Djacobse
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Probe Design

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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

  1. Obtain transcript sequence from Genome Browser
    1. Use genome browser to find genes, and tables to download transcript (mRNA only)
  2. Use gene sequence as input for probe designer
    1. Designer created by Arjun Raj, utilized by Long Cai for paper
    2. Creates 20mer probes
  3. Copy/paste probe sequences into .txt file
  4. Print only sequence to the oligo file
    1. awk '{print $2}' malat1_probes.txt > oligos_malat1.txt
  5. Attach primer sequences before/after
    1. VI command, forward: :%s!^!GTCATATCGGTCACTGTT!
    2. VI command, reverse: :g/$/norm AGATCAGGATACACACTACCC
    3. Primer sequences are AP1 and AP2 from the V6 set, used in High Resolution Chromosome Painting