Hosuk:LabNotes/2013-11-21: Difference between revisions
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| align="center" | MALAT1 || align="center" | 4886 || align="center" | 4196 || align="center" | 3817 || align="center" | 4155 || align="center" | 6179 || align="center" | 5561 | | align="center" | MALAT1 || align="center" | 4886 || align="center" | 4196 || align="center" | 3817 || align="center" | 4155 || align="center" | 6179 || align="center" | 5561 | ||
|- | |- | ||
| align="center" | % || align="center" | 66.14 || align="center" | 64.60 || align="center" | 63.20 || align="center" | 68.24 || align="center" | 87.60 || align="center" | 64.19 | | align="center" | % || align="center" | 66.14 || align="center" | 64.60 || align="center" | 63.20 || align="center" | 68.24 || align="center" | 87.60 || align="center" | 64.19 | ||
|} | |||
{| {{table}} border = 1 | |||
| align="center" style="background:#f0f0f0;"|'''Dye Probes''' | |||
| align="center" style="background:#f0f0f0;"|'''Pos3''' | |||
| align="center" style="background:#f0f0f0;"|'''Pos4''' | |||
| align="center" style="background:#f0f0f0;"|'''Pos5''' | |||
| align="center" style="background:#f0f0f0;"|'''Pos2''' | |||
| align="center" style="background:#f0f0f0;"|'''Pos1''' | |||
| align="center" style="background:#f0f0f0;"|'''Pos6''' | |||
|- | |||
| align="center" | Aligning | |||
| align="center" | 0.1nM | |||
| align="center" | 1nM | |||
| align="center" | 10nM | |||
| align="center" | 100nM | |||
| align="center" | 5uM | |||
| align="center" | 5uM | |||
|- | |||
| align="center" | offset || align="center" | x = -9, y = -43 || align="center" | || align="center" | || align="center" | || align="center" | || align="center" | | |||
|- | |||
| align="center" | Crop || align="center" | 51 by 51px || align="center" | || align="center" | || align="center" | || align="center" | || align="center" | | |||
|- | |||
| align="center" | 1st Rolony || align="center" | 6742 || align="center" | || align="center" | || align="center" | || align="center" | || align="center" | | |||
|- | |||
| align="center" | MALAT1 || align="center" | 5528 || align="center" | || align="center" | || align="center" | || align="center" | || align="center" | | |||
|- | |||
| align="center" | Overlapped || align="center" | 4465 || align="center" | || align="center" | || align="center" | || align="center" | || align="center" | | |||
|- | |- | ||
| align="center" | | | align="center" | % || align="center" | 66.23 || align="center" | || align="center" | || align="center" | || align="center" | || align="center" | | ||
|- | |- | ||
|} | |} | ||
Revision as of 06:47, 22 November 2013
Padlock Probe Concentration Test
- Sample : 96 well plates, made at 10/23
- 2048 x 2048, 600Hz
- Each stripping : 30min, and annealing : 15min
- The concentration of the dye-labeled probe : 1uM
- Use “Mark and Fine” function to save each location at each well
Procedure
- Process Steps
- Step 1 : Image 1st Rolony
- Step 2 : Strip, anneal ppMATLA1 (0.1nM, 1nM, 10nM, 100nM, and 5uM)
- Step 3 : Add “Shifted FISSEQ_2ndRCAprimerDye” , image
Result
- Need overlap counting, but
- 0.1nM of padlock probe seemed many signal, and Need to plat toe…
- Will do more further analysis
1st Rolony Count
- Pos 6 : for strip test
Pos 6, 5uM | Pos 1, 5uM | Pos 2, 100nM |
Pos 5, 10nM | Pos 4, 1nM | Pos 3, 0.1nM |
Counting
- px : 2~100, bkmulti = 13
Dye Probes | Pos3 | Pos4 | Pos5 | Pos2 | Pos1 | Pos6 |
0.1nM | 1nM | 10nM | 100nM | 5uM | 5uM | |
1st Rolony | 7387 | 6495 | 6040 | 6089 | 7054 | 8663 |
MALAT1 | 4886 | 4196 | 3817 | 4155 | 6179 | 5561 |
% | 66.14 | 64.60 | 63.20 | 68.24 | 87.60 | 64.19 |
Dye Probes | Pos3 | Pos4 | Pos5 | Pos2 | Pos1 | Pos6 |
Aligning | 0.1nM | 1nM | 10nM | 100nM | 5uM | 5uM |
offset | x = -9, y = -43 | |||||
Crop | 51 by 51px | |||||
1st Rolony | 6742 | |||||
MALAT1 | 5528 | |||||
Overlapped | 4465 | |||||
% | 66.23 |
Workflow
- In order to match work area in both 1st rolony image and ppMALAT1 image after global aligning