Noi/NOTES/2012-7-31: Difference between revisions

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[[http://genome-tech.ucsd.edu/LabNotes/index.php/noi:DMR220k_LabNotes '''Link to calendar''']]<br>
[[http://genome-tech.ucsd.edu/LabNotes/index.php/noi:DMR220k_LabNotes '''Link to calendar''']]<br>
= Preparation of sheared gDNA for N37 sample set =
= Preparation of sheared gDNA for N37 sample set =
* Alice make an appointment with James at Biogen  
* Alice makes an appointment with James at Biogen  
'''Sample list and code on the tube'''
'''Sample list and code on the tube'''
* From the previous experiment, gDNA of the 10 tissues of N37 were diluted to 100ng/ul total volume 20ul. I used 12 ul for BSPP assays, and have 8ul left.
* From the previous experiment, gDNA of the 10 tissues of N37 were diluted to 100ng/ul total volume 20ul. I used 12 ul for BSPP assays, and have 8ul left.
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|-
|-
| N37Stomach||N37-10||~100||2.00||48.00||50.00
| N37Stomach||N37-10||~100||2.00||48.00||50.00
|}
|}<br>
   '''Follow up the set up for Covaris shearing (From BioGem and Alan's note''': [[http://genome-tech.ucsd.edu/LabNotes/index.php/AlanFung:LabNotes/Methylome/2012-1-17]]
* Sheared on 2012.08.01
   '''Follow up the set up for Covaris shearing (From BioGem and Alan's note''': [[http://genome-tech.ucsd.edu/LabNotes/index.php/AlanFung:LabNotes/Methylome/2012-1-17]])
  Target BP 400
  Target BP 400
  Tube Micro
  Tube Micro

Revision as of 22:46, 3 August 2012

[Link to calendar]

Preparation of sheared gDNA for N37 sample set

  • Alice makes an appointment with James at Biogen

Sample list and code on the tube

  • From the previous experiment, gDNA of the 10 tissues of N37 were diluted to 100ng/ul total volume 20ul. I used 12 ul for BSPP assays, and have 8ul left.
  • I need to check if there is some evaporation and need to bring total volume to 8ul with EB buffer.
  • I plan to shear 200ng of gDNA, so I will take 2ul of gDNA and add to 48ul of H2O.
  • The total volume reduced to ~5ul, I added 3ul to each tube to bring volume up to 8ul
Sample IDs Sample code on tubes Original conc. (ng/ul) Volume
for 200ng (ul)
EB (ul) Total volume (ul)
N37-Cerebellum (CRBL) N37-1 ~100 2.00 48.00 50.00
N37-Colon N37-2 ~100 2.00 48.00 50.00
N37-Frontal lobe (FL) N37-3 ~100 2.00 48.00 50.00
N37-Heart N37-4 ~100 2.00 48.00 50.00
N37-Small intestine (SI) N37-5 ~100 2.00 48.00 50.00
N37-Liver N37-6 ~100 2.00 48.00 50.00
N37-Lung N37-7 ~100 2.00 48.00 50.00
N37-Skeletal muscle (SM) N37-8 ~100 2.00 48.00 50.00
N37Pancrease N37-9 ~100 2.00 48.00 50.00
N37Stomach N37-10 ~100 2.00 48.00 50.00


  • Sheared on 2012.08.01
 Follow up the set up for Covaris shearing (From BioGem and Alan's note: [[1]])
Target BP 400
Tube Micro
Duty Factor 10%
Peak Incident Power (w) 140
Cycle per Burst 200
Time (secs) 55
Volume 50ul
Temperature (c) 7 
Intensifier Yes