Noi/NOTES/2012-5-16: Difference between revisions

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* Continued from: http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-5-14
* Continued from: http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-5-14
* Since Dr. Zhang suggested that about 20% of the oligos having AP2 part should be fine. I will continue to digest the rest of amplified amplicons with DpnII and column purify
* Since Dr. Zhang suggested that about 20% of the oligos having AP2 part should be fine. I will continue to digest the rest of amplified amplicons with DpnII and column purify
   Probe IDs       Conc. (ng/ul) Yields in 120ul (ug) Left over after trial (ug)
   Probe IDs   Conc. (ng/ul) Yields in 120ul (ug) Left over after trial (ug)
  #1-V4           83.70         10.04                   5.00
  #1-V4         83.70         10.04                 5.00
  #2-V4         125.10         15.01                 12.00
  #2-V4         125.10         15.01                 12.00
  #3-V4         110.10         13.21                 13.20
  #3-V4         110.10         13.21                 13.20
Line 12: Line 12:
  #3-V6         132.20         15.86                 15.86
  #3-V6         132.20         15.86                 15.86
  #4-V6         101.70         12.20                 12.20
  #4-V6         101.70         12.20                 12.20
'''DpnII digestion reaction set up'''
{| {{table}} border = 1
| align="center" style="background:#f0f0f0;"|'''Probe IDs'''
| align="center" style="background:#f0f0f0;"|'''Conc. (ng/ul)'''
| align="center" style="background:#f0f0f0;"|'''Volume (ul)'''
| align="center" style="background:#f0f0f0;"|'''H2O (ul)'''
| align="center" style="background:#f0f0f0;"|'''10X DpnII Buffer'''
| align="center" style="background:#f0f0f0;"|'''DpnII'''
| align="center" style="background:#f0f0f0;"|'''Total volume (ul)'''
| align="center" style="background:#f0f0f0;"|'''# of tube'''
|-
| #1-V4||83.70||59.74||22.26||10||8||100.00||1
|-
| #2-V4||125.10||47.96||34.04||10||8||100.00||2
|-
| #3-V4||110.10||59.95||22.05||10||8||100.00||2
|-
| #4-V4||133.80||59.79||22.21||10||8||100.00||1
|-
| #1-V6||122.50||60.00||22.00||10||8||100.00||2
|-
| #2-V6||106.20||59.98||22.02||10||8||100.00||2
|-
| #3-V6||132.20||59.98||22.02||10||8||100.00||2
|-
| #4-V6||101.70||59.98||22.02||10||8||100.00||2
|}
37C 30min -> 65C 20min -> Qiaquick column purification (also combine the samples used for DpnII digestion trial.
Measure concentration by Nanodrop and calculate yield

Revision as of 20:27, 16 May 2012

Probe production for the HiResChrPaint project

 Probe IDs    Conc. (ng/ul) Yields in 120ul (ug) Left over after trial (ug)
#1-V4	         83.70	         10.04	                 5.00
#2-V4	        125.10	         15.01	                12.00
#3-V4	        110.10	         13.21	                13.20
#4-V4	        133.80	         16.06	                 8.00
#1-V6	        122.50	         14.70	                14.70
#2-V6	        106.20           12.74	                12.74
#3-V6	        132.20	         15.86	                15.86
#4-V6	        101.70	         12.20	                12.20
DpnII digestion reaction set up
Probe IDs Conc. (ng/ul) Volume (ul) H2O (ul) 10X DpnII Buffer DpnII Total volume (ul) # of tube
#1-V4 83.70 59.74 22.26 10 8 100.00 1
#2-V4 125.10 47.96 34.04 10 8 100.00 2
#3-V4 110.10 59.95 22.05 10 8 100.00 2
#4-V4 133.80 59.79 22.21 10 8 100.00 1
#1-V6 122.50 60.00 22.00 10 8 100.00 2
#2-V6 106.20 59.98 22.02 10 8 100.00 2
#3-V6 132.20 59.98 22.02 10 8 100.00 2
#4-V6 101.70 59.98 22.02 10 8 100.00 2
37C 30min -> 65C 20min -> Qiaquick column purification (also combine the samples used for DpnII digestion trial.
Measure concentration by Nanodrop and calculate yield