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);