Matt:LabNotes/2013-6-26: Difference between revisions

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===Page Size Selection of 0 gap probes===
===Page Size Selection of 0 gap probes===
USER/DpnII digested 0 gap probes:
USER/DpnII digested 0 gap probes:
   Noi made 11.36ug/400ul [http://genome-tech.ucsd.edu/LabNotes/index.php/Matt:LabNotes/2013-5-29]
   Noi made 11.36ug/~400ul [http://genome-tech.ucsd.edu/LabNotes/index.php/Matt:LabNotes/2013-5-29]
   I made 10.58ug/180ul [http://genome-tech.ucsd.edu/LabNotes/index.php/Matt:LabNotes/2013-5-16]
   I made 10.58ug/180ul [http://genome-tech.ucsd.edu/LabNotes/index.php/Matt:LabNotes/2013-5-16]
   <!--If Combined: 11.36ug + 10.58ug / (410ul + 180ul) = 21.94ug/590ul = 37.19ng/ul (590ul)-->
   <!--If Combined: 11.36ug + 10.58ug / (410ul + 180ul) = 21.94ug/590ul = 37.19ng/ul (590ul)-->


To run ~3ug/gel, I use 100ul of probes that Noi made for each of the 4 gels
To run ~3ug/gel, I use ~100ul of probes that Noi made for each of the 4 gels


* Ran TBU gel at 220V for 30 min with samples and ladder prepared below
* Ran TBU gel at 220V for 30 min with samples and ladder prepared below
Line 16: Line 16:
| align="center" style="background:#f0f0f0;"|'''4X Volume'''
| align="center" style="background:#f0f0f0;"|'''4X Volume'''
|-
|-
| Enzyme digested probes (~11.36/400ul)||100||400
| Enzyme digested probes (~11.36/400ul)||106||424
|-
|-
| TBE-Urea Buffer 2X||100||400
| TBE-Urea Buffer 2X||106||424
|-
|-
| H2O||0||0
| H2O||0||0
|-
|-
| Total||200||800
| Total||212||848
|-
|-
|  
|  

Revision as of 18:39, 26 June 2013

Page Size Selection of 0 gap probes

USER/DpnII digested 0 gap probes:

 Noi made 11.36ug/~400ul [1]
 I made 10.58ug/180ul [2]

To run ~3ug/gel, I use ~100ul of probes that Noi made for each of the 4 gels

  • Ran TBU gel at 220V for 30 min with samples and ladder prepared below
    • Heated TBE buffer in microwave
    • Denatured samples/ladder for 10 min at 75C before putting on cold rack for 1 min
    • Size selected for brightest band below 200bp
Components 1X Volume 4X Volume
Enzyme digested probes (~11.36/400ul) 106 424
TBE-Urea Buffer 2X 106 424
H2O 0 0
Total 212 848
Components 1X Volume 4X Volume
10-bp DNA ladder (1 ug/ul) 1 4
TBE-Urea Buffer 2X 5 20
H2O 4 16
total 10 40