Jie:LabNotes/CpgSeq/2009-8-27: Difference between revisions

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  chr20:60061824 on PGP3L and PGP9L;
  chr20:60061824 on PGP3L and PGP9L;
  chr20:60403281 on PGP1L and PGP3L;  
  chr20:60403281 on PGP1L and PGP3L;  
chr20:31718894_rs3746459 on BJ;


                                                           x 8
                                                           x 9
  2x iQ supermix                          50            400          
  2x iQ supermix                          50            450          
  Primer F (50uM) 0.5         0.5 each
  Primer F (50uM) 0.5         0.5 each
  Primer R (50uM) 0.5            0.5 each
  Primer R (50uM) 0.5            0.5 each
  sample bis-gDNA (~202ng/ul)            0.1   0.1 each
  sample bis-gDNA (~202ng/ul)            0.1   0.1 each
  dH2O         50 400
  dH2O         50 450
  total         40ul
  total         40ul


  96C 3min-> 45x (95C 30sec, MATN4 and DNMT3B at 58C, rs10846023 on 62C 1min, 72C 1min)-> 72C 5min.
  96C 3min-> 45x (95C 30sec, 62C 1min, 72C 1min)-> 72C 5min.
 
[[image:20090827_cell_and_individual_ASM.jpg|500px]]20090827_cell and individual ASM
 
I get the amplicons from all 9 samples except chr20:60403281 on PGP1L and PGP3L.
 
==TA cloning of 7 samples==
I did TA cloning for
chr12:4541690_rs34206253 on PGP1L and PGP1F;
chr21:32746340_rs8128908 on PGP1L and PGP1F;
chr20:60061824_rs6061990 on PGP3L and PGP9L;
chr20:31718894_rs3746459 on BJ;
 
==Plates to agencourt==
rs6061990_PGP3L_PGP9L_rs3746459_BJ;
MATN4_PGP1F_PGP1iPS_rs10846023_BJ;
DNMT3B_PGP3L_PGP9L_rs34206253_PGP1L;
rs8128908_PGP1L_PGP1F_rs34206253_PGP1F_MMP9_PGP1L (Row A~B are rs8128908_PGP1L, C1~E8 are rs8128908_PGP1F, E9~H4 are rs3406253_PGP1F, H5~H12 are MMP9_PGP1L);

Latest revision as of 17:46, 28 September 2009

ASM validation of cell type and individual dependent ASM[edit]

primers for cell and individual dependent ASM validation 
I did the PCR using 2x iQ supermix on:

chr12:4541690 on PGP1L and PGP1F;
chr21:32746340 on PGP1L and PGP1F;
chr20:60061824 on PGP3L and PGP9L;
chr20:60403281 on PGP1L and PGP3L; 
chr20:31718894_rs3746459 on BJ;
                                                         x 9
2x iQ supermix                          50             450          
Primer F (50uM)			 0.5	        0.5 each
Primer R (50uM)			 0.5            0.5 each
sample bis-gDNA (~202ng/ul)             0.1	  	0.1 each
dH2O				         50		450
total				         40ul
96C 3min-> 45x (95C 30sec, 62C 1min, 72C 1min)-> 72C 5min.
File:20090827 cell and individual ASM.jpg20090827_cell and individual ASM
I get the amplicons from all 9 samples except chr20:60403281 on PGP1L and PGP3L.

TA cloning of 7 samples[edit]

I did TA cloning for 
chr12:4541690_rs34206253 on PGP1L and PGP1F;
chr21:32746340_rs8128908 on PGP1L and PGP1F;
chr20:60061824_rs6061990 on PGP3L and PGP9L;
chr20:31718894_rs3746459 on BJ;

Plates to agencourt[edit]

rs6061990_PGP3L_PGP9L_rs3746459_BJ;
MATN4_PGP1F_PGP1iPS_rs10846023_BJ;
DNMT3B_PGP3L_PGP9L_rs34206253_PGP1L;
rs8128908_PGP1L_PGP1F_rs34206253_PGP1F_MMP9_PGP1L (Row A~B are rs8128908_PGP1L, C1~E8 are rs8128908_PGP1F, E9~H4 are rs3406253_PGP1F, H5~H12 are MMP9_PGP1L);