Daniel:Notebook/RNAFISH/2014-7-11

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Revision as of 19:34, 11 July 2014 by >Djacobse
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Probe Design

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Probe List

Rui sent me a list of genes to design probes for. Here it is:

  • GRIK4 Glutamate Receptor, IK-4
  • GPC6 HS glypican -coreceptor for growth factors
  • ERBB4 ERBB4
  • GRIK1 Glutamate receptor, IK-1
  • DNER Notch-like grow factor receptor
  • DCC netrin 1 receptor
  • POU6F2 POU TF
  • FOXP2 TF
  • GAD1 glutamate decarboxylase 1
  • GAD2 glutamate decarboxylase 2
  • CA10 carbonic anhydrase

Workflow

  1. Identify genomic coordinates using UCSC genome browser, hg38
  2. Download the CDS Exon sequence using the tables tab of the genome browser
  3. Run MATLAB script that outputs only the sequence can also trim the sequence to 8kbp (Stellaris maximum)
    1. MATLAB script
  4. Paste sequence into Stellaris website
    1. Currently using 25 probes per gene
  5. Copy/paste sequences into a .txt file