Hosuk:LabNotes/2014-8-29
Jump to navigation
Jump to search
Decoding PGP1F with Agi26k0gap Padlock Probe – 2nd full decoding[edit]
Sample[edit]
- This PGP1F MatTek dish was
- S2, 1st rolonies made at 2014-04-10
- 2nd rolonies finished at 2014-04-14
- 2 color dye + 5 cycle decoding done at 2014-04-14
- Matt run 7 cycle decoding - 2014-08-28
- Data stored 2014-08-28 folder
Procedure[edit]
- Align all images based on BF
- Shift and crop images of every steps, make MIP image with all steps of aligned and cropped images
- Count 1st Rolony by PISA
- Count 1st Rolony and make BW image from MIP of all step images by PISA
- PISA param test and apply
- PISA parameter
- PISAParam.log_radius = 3;
- PISAParam.log_upper = -2e-4;
- PISAParam.area_upper = 100;
- PISAParam.area_lower = 10;
- PISAParam.axratio_lower = 0.5;
- PISAParam.circ_upper = 1.6;
- PISAParam.circ_lower = 0.8;
- PISAParam.pconn = 8;
- PISAParam.bkgmult_lower = 3;
- PISAParam.FilterOption = 1;
- PISAParam.Deconvoluted = 0;
- PISAParam.DoMedflt = 1;
- PISAParam.nofindbkg = 0;
- Run Script (will be specified later...)
Result[edit]
- Result
- Number of cells : Pos1 ~ 120, Pos2 : 100
- 1st Rolony :
- Pos1 : 31371, 261.43/cell
- Pos2 : 27354, 273.54/cell
- MIP of all steps :
- Pos1 : 6621, 55.18/cell
- Pos2 : 4739, 47.39/cell
- Even if 2nd full decoding sample has more 1st rolonies, it has less number of decoded features…
- To DO : Decode this with 63x!!!, and compare RNA expression data from Jay’s or Zhang Lab’s
Comparison of 1st rolonies between 1st decoding and 2nd decoding[edit]
Decoded counts and gene mapping table : position 1[edit]
File:DecodeResult MarkBarcode Pos1 2014-08-29.png
Decoded counts and gene mapping table : position 2[edit]
File:DecodeResult MarkBarcode Pos2 2014-08-29.png