Matt:LabNotes/2016-4-8

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Revision as of 03:02, 13 April 2016 by >Mzcai (Created page with "=Design Padlock Probe Arms for Mouse and Human Housekeeping Gene Probe Set= *For DARTFISH in human and mouse tissues, we are most interested in seeing the heterogeneity and va...")
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Design Padlock Probe Arms for Mouse and Human Housekeeping Gene Probe Set

  • For DARTFISH in human and mouse tissues, we are most interested in seeing the heterogeneity and variation in gene expression
  • However, to distinguish biological variation from technical noise it would be nice to have some probes for genes that are uniformly detected in each tissue


  • Files: Dropbox\GradZhangLab\CA12k_Apr2016\ControlGenes\MouseEmbryo and Dropbox\GradZhangLab\CA12k_Apr2016\ControlGenes\HumanBrain

Mouse Embryo

Gene Selection

  • "high_genes_mouse_project.xls" contains 54 high expression genes with lowest variance (variance included)
  • Selected top 25 lowest variance genes "Top25_LowVarGenes.txt"
    • Includes Gapdh and Actg

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