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===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: [[Hosuk:LabNotes/2013-9-26]] *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 {| {{table}} | align="center" style="background:#f0f0f0;"|'''ID_REF''' | align="center" style="background:#f0f0f0;"|'''VALUE''' | align="center" style="background:#f0f0f0;"|'''STDERR''' | align="center" style="background:#f0f0f0;"|'''BEADN''' | align="center" style="background:#f0f0f0;"|'''PVAL''' | align="center" style="background:#f0f0f0;"|'''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
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