Matt:LabNotes/2013-9-26: Difference between revisions

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===New Gene for Secondary Rolony===
===New Gene for Secondary Rolony===
*Image of ACTB probe targeting primary rolonies revealed maybe not enough ACTB
*Image of ACTB probe targeting primary rolonies revealed maybe not enough ACTB
**Look for new gene
**In a frame with over a thousand primary rolonies, there were maybe 10-15 ACTB probe targets
 
*Below is my work for identifying a new gene with many RNA transcripts and designing a padlock probe for it


*Using microarray data for PGP1F referenced here: [[Matt:LabNotes/2013-9-25#Expected_number_of_ACTB_and_RAB7A_Rolonies]] found the genes with highest expression levels
*Using microarray data for PGP1F referenced here: [[Matt:LabNotes/2013-9-25#Expected_number_of_ACTB_and_RAB7A_Rolonies]] found the genes with highest expression levels
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| ILMN_1765043||51370.86||1379.863||34||0||RPL38
| 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
*Entered entrez IDs into Biomart to make: mart_export_BeadchipHighExprGenes.txt
*Added entrez IDs into 13th column to make ConstitutiveExonFinderInput_BeadchipHighExprGenes.txt
*Added entrez IDs into 13th column to make ConstitutiveExonFinderInput_BeadchipHighExprGenes.txt

Revision as of 21:48, 27 September 2013

New Gene for Secondary Rolony

  • Image of ACTB probe targeting primary rolonies revealed maybe not enough ACTB
    • In a frame with over a thousand primary rolonies, there were maybe 10-15 ACTB probe targets
  • 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