Matt:LabNotes/2013-9-26

From ZhangLabWiki
Jump to navigation Jump to search

New Gene for Secondary Rolony[edit]

  • Image of ACTB probe targeting primary rolonies revealed maybe not enough ACTB
  • Below is my work for identifying a new gene with many RNA transcripts and designing a padlock probe for it
ID_REF VALUE STDERR BEADN PVAL Gene
ILMN_1746516 55290.05 1605.329 41 0 RPS25
ILMN_2053178 54348.41 1365.424 52 0 ACTG
ILMN_1708934 52141.46 1374.303 32 0 ADM
ILMN_1723978 52038.04 1305.076 43 0 LGALS1
ILMN_1765043 51370.86 1379.863 34 0 RPL38
  • For reference, ACTB (ILMN_2152131) ranks 50th with 42,723.45 and ACTB (ILMN_2038777) ranks 85th with 33,579.69. RAB7A is 638th (ILMN_1716524) with 7,254.7
  • Entered entrez IDs into Biomart to make: mart_export_BeadchipHighExprGenes.txt
  • Added entrez IDs into 13th column to make ConstitutiveExonFinderInput_BeadchipHighExprGenes.txt
  • Created genes_BeadchipHighExprGenes.txt
  • Ran ConstitutiveExonFinder.pl > TargetFile_BeadchipHighExprGenes.txt
  • Sort with sortTargetFilesByChr.pl > targetFile_chr{11,17,22}.txt
  • Run ppDesigner.pl
 perl ../src/ppDesigner.pl jobFile_chr11.pl > outputFile_chr11.txt
 perl ../src/ppDesigner.pl jobFile_chr17.pl > outputFile_chr17.txt
 perl ../src/ppDesigner.pl jobFile_chr22.pl > outputFile_chr22.txt
  • Combine files to outputFile_BeadchipHighExprGenes_1gap.txt
  • Convert to 0gap probe: ConvertToZeroGapProbe.pl > outputFile_BeadchipHighExprGenes_0gap.txt
  • Based on Overlap Transcript Ratio in TargetFile_BeadchipHighExprGenes.txt, the designed probes with most overlap are