Hosuk:LabNotes/2014-2-9

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Revision as of 20:38, 10 February 2014 by >Hosuki78
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NCIH1975 : Mutation Detection : 2nd Try, Data Analysis

  • Data from 2/3
  • Took pictures at 3 Positions on the sample in MatTek dish

Procedure

    1. Maximum projection image with all images of 8 steps
    2. Run PISA to make BW images
    3. Use the BW image as mask image file and do masking an each image (=image file .* mask image)
    4. Run PISA with masked image, and obtain a number of rolonies, centroid coordinate information of each rolony
    5. Decode the rolony to extract decoding information along steps


Major Parameters

Decode Binary table of each target
EGFR_T790M_WT EGFR_T790M_MU EGFR_L858R_WT EGFR_L858R_MU
Step1 (1FAM) 0 1 0 1
Step2 (1Cy3) 1 0 0 0
Step3 (2FAM) 0 0 1 0
Step4 (2Cy3) 0 0 0 1
Step5 (3FAM) 1 0 1 0
Step6 (3Cy3) 0 1 0 0
Step7 (4FAM) 1 0 0 1
Step8 (4Cy3) 0 1 1 0


Decode Binary String of each target
  • EGFR_T790M_WT = '01010010'
  • EGFR_T790M_MU = '10100001'
  • EGFR_L858R_WT = '10010100'
  • EGFR_L858R_MU = '01001001'


Allowing 1 bit Error cases of Decode Binary String
  • EGFR_T790M_WT
    • Normal : '01010010'
    • Error 1 : '01010000'
    • Error 2 : '01000010'
    • Error 3 : '00010010'


  • EGFR_T790M_MU
    • Normal : '10100001'
    • Error 1 : '10100000'
    • Error 2 : '10000001'
    • Error 3 : '00100001'


  • EGFR_L858R_WT
    • Normal : '10010100'
    • Error 1 : '10010000'
    • Error 2 : '10000100'
    • Error 3 : '00010100'


  • EGFR_L858R_MU
    • Normal : '01001001'
    • Error 1 : '01001000'
    • Error 2 : '01000001'
    • Error 3 : '00001001'


Result

Counts
Target Pos 1 Pos 2 Pos 3 Avg Std
EGFR_T790M_WT
01010010 4 2 6 4 2
01010000 5 14 16 11.67 5.86
01000010 3 2 1 2 1
00010010 4 12 10 8.67 4.16
EGFR_T790M_MU
10100001 0 0 2 0.67 1.15
10100000 1 1 2 1.33 0.58
10000001 1 1 0 0.67 0.58
00100001 0 0 0 0 0
EGFR_L858R_WT
10010100 3 6 8 5.67 2.52
10010000 5 11 18 11.33 6.51
10000100 4 7 5 5.33 1.53
00010100 2 28 22 17.33 13.61
EGFR_L858R_MU
01001001 0 0 0 0 0
01001000 0 0 1 0.33 0.58
01000001 17 12 6 11.67 5.51
00001001 1 0 1 0.67 0.58


Data Files