Matt:LabNotes/2013-9-26
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New Gene for Secondary Rolony[edit]
- 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
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