Rui:Haplotying: Difference between revisions

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>RuiLiu
>RuiLiu
Line 17: Line 17:
  0.2% TritonX-100
  0.2% TritonX-100
  (0.1 AU/ml Qiagen Proteinase 7.5AU)
  (0.1 AU/ml Qiagen Proteinase 7.5AU)


Step 2: Proteinase and aliquot
Step 2: Proteinase and aliquot


Add Proteinase right before aliquot, 1ul per tube, to 20 tubes. Store at -80C.
Add Proteinase right before aliquot, 1ul per tube, to 20 tubes. Store at -80C.


Step 3: gDNA Tagmentation
Step 3: gDNA Tagmentation
Line 33: Line 35:


55C for 5min
55C for 5min
Quick spin and cool down on ice
Quick spin and cool down on ice


Step 4: Addition of T7 adaptor by Kapa system (?)
Step 4: Addition of T7 adaptor by Kapa system (?)


  Tagmented gDNA         5ul
  Tagmented gDNA         5ul
  Kapa master mix 10ul
  Kapa master mix       1X
  (dNTP;polymerase)
  (dNTP;polymerase)
  0.5uM T7 adaptor 1ul
  0.5uM T7 adaptor 1ul
  100* SYBR green 0.25ul
  100* SYBR green       0.25ul
  Nf water         up to 50ul  
  Nf water         up to 50ul  
  '''Total                 50ul
  '''Total         50ul'''
'''
 
72C, 3min; 95C, 30sec
 
95C, 10sec; 62C, 30sec; 72C, 3min; 5 cycles
 
 
Step 5: ExoI (SAP) treatment (?)
 
Removal of T7 adaptor is a must for IVT, maybe optional for PCR as the following step...
 
10U/ul ExoI mixed with 1U/ul SAP as 1.5~5U:1U, add 2ul (?) for each tube
 
37C, 30min; 80C, 15-25min
 
 
Step 6: Mix and EtOH precipitation
 
Mix 10 tubes (~500ul) for EtOH precipitation
 
Glycoblue  2ul
NaOAc     50ul
EtOH      1250ul
'''Total  1800ul'''


==Primers==
==Primers==

Revision as of 23:46, 16 March 2011

Background

Original: File:Design.ppt

Modified: File:Tn-based-haplotyping V1.1.ppt

Protocol

Step 1: Cell lysis

Collect 10 cells in 20ul lysis buffer.

Cell lysis buffer (1*)
200mM NaCl
20mM EDTA
10mM Tris-HCl (pH 8)
0.2% TritonX-100
(0.1 AU/ml Qiagen Proteinase 7.5AU)


Step 2: Proteinase and aliquot

Add Proteinase right before aliquot, 1ul per tube, to 20 tubes. Store at -80C.


Step 3: gDNA Tagmentation

  • 1:50 dilution of Nextera transposomes: 1ul Nextera enzyme in 24ul TE and 25ul 100% Glyceral
gDNA	        1ul
5X HMW buffer	1ul
transposomes	1ul
Nf water	2ul
Total 	        5ul

55C for 5min

Quick spin and cool down on ice


Step 4: Addition of T7 adaptor by Kapa system (?)

Tagmented gDNA	        5ul
Kapa master mix        1X
(dNTP;polymerase)	
0.5uM T7 adaptor	1ul
100* SYBR green        0.25ul
Nf water 	        up to 50ul 
Total	        50ul

72C, 3min; 95C, 30sec

95C, 10sec; 62C, 30sec; 72C, 3min; 5 cycles


Step 5: ExoI (SAP) treatment (?)

Removal of T7 adaptor is a must for IVT, maybe optional for PCR as the following step...

10U/ul ExoI mixed with 1U/ul SAP as 1.5~5U:1U, add 2ul (?) for each tube

37C, 30min; 80C, 15-25min


Step 6: Mix and EtOH precipitation

Mix 10 tubes (~500ul) for EtOH precipitation

Glycoblue  2ul
NaOAc	    50ul
EtOH       1250ul
Total   1800ul

Primers

File:Primers for Tn-based-haplotyping.xls

2011

<calendar> name=Rui:LabNotes/Haplotyping format=%name/%year-%month-%day date=2011/10/1 view=oneyear </calendar>