Jie:LabNotes/CpgSeq/2009-8-27

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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);