Matt:LabNotes/2016-4-6

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Revision as of 00:49, 7 April 2016 by >Mzcai (Created page with "=Design Padlock Probe Arms for new Probe Set= *Design probes for genes that reveal heterogeneity in mouse brain *Genes are specific for certain cell types and subtypes determi...")
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Design Padlock Probe Arms for new Probe Set

  • Design probes for genes that reveal heterogeneity in mouse brain
  • Genes are specific for certain cell types and subtypes determined by Allen Brain Institute collaborators
  • Files: Dropbox\GradZhangLab\CA12k_Apr2016\MouseBrain

Gene Selection

  • 152 genes: GeneListv1.txt
    • 2310042E22Rik -> Teddm3 (MGI Symbol)
    • 6330527O06Rik -> Lamp5 (MGI Symbol)
    • A930038C07Rik -> Ndnf (MGI Symbol)
    • Ppapdc1a -> Plpp4 (MGI Symbol)
    • Gpr126 -> Adgrg6 (MGI Symbol)
    • Fam5c -> Brinp3 (MGI Symbol)


Get Transcript Sequences

  • Biomart browser interface
 Dataset
 Mus musculus genes (GRCm38.p4)
 Filters
 with MGI ID(s): Only
 MGI symbol [e.g. Mir1901]: [ID-list specified]
 Status (gene): KNOWN
 Status (transcript): KNOWN
 Attributes
 Ensembl Gene ID
 Ensembl Transcript ID
 Chromosome Name
 Exon Rank in Transcript
 Exon Chr Start (bp)
 Exon Chr End (bp)
 Strand
 Associated Gene Name
  • 151 Unique Ensembl Gene IDs and Associated Gene Names
    • Missing 9630013A20Rik

Create ppDesigner Target Files

  • Files in genome-miner:~/scratch/CA12kApr2016_ProbeDesign/MouseBrain
  • Use CreateTargetFile_contig.pl to create target file where targets are contigs of exons
    • Script is modified from here
  • Sort target files into each chromosome and remove 25bp from each end of target and switch strand
    • SortTargetFilesByChr.pl

Run ppDesigner

ppDesignerCommands.sh

  1. !/bin/bash

for indx in 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 X do /home/mzcai/scratch/CA12kApr2016_ProbeDesign/MouseBrain/opt/ppDesigner/src/ppDesigner.pl /home/mzcai/scratch/CA12kApr2016_ProbeDesign/MouseBrain/jobFile_chr$indx.pl > /home/mzcai/scratch/CA12kApr2016_ProbeDesign/MouseBrain/outputFile_chr$indx.txt & wait done