Alice:LabNotes/2007-12-5

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Revision as of 07:01, 1 January 2008 by >Zsakura2
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The sequencing results finally worked!

Sample SNP Sequencing result
1 rs3753565 yes
2 rs2295680 yes
3 rs6103 no
4 rs1264899 yes
5 rs1264899 yes
6 rs1264899 yes
7 rs1264899 yes

Sample 1
File:SNP 1.png

Sample peak location base pair base pair peak value
ZL1-cust.ab1 92 N C 255
ZL1-cust.ab1 94 C C 695
ZL1-cust.ab1 92 N T 214
ZL1-cust.ab1 93 T T 613

peak ratio: 255+695 : 214+613 = 950 : 827

Sample 2
File:SNP 2.png

Sample peak location base pair base pair peak value
ZL2-cust.ab1 96 A G 190
ZL2-cust.ab1 94 G G 724
ZL2-cust.ab1 96 A A 209
ZL2-cust.ab1 95 A A 647

peak ratio: 190+724 : 209+647 = 914 : 856
Sample 4
File:SNP 4.png

Sample peak location base pair base pair peak value
ZL4-cust.ab1 88 C C 763
ZL4-cust.ab1 89 C C 731
ZL4-cust.ab1 88 C T 58
ZL4-cust.ab1 87 T T 475

peak ratio: 763+731 : 58+475 = 1494 : 533
Sample 5
File:SNP 5.png

Sample peak location base pair base pair peak value
ZL5-cust.ab1 87 T T 386
ZL5-cust.ab1 86 T T 342
ZL5-cust.ab1 87 T C 161
ZL5-cust.ab1 88 C C 583

peak ratio: 386+342 : 161+583 = 728 : 744
Sample 6
File:SNP 6.png

Sample peak location base pair base pair peak value
ZL6-cust.ab1 150 T T 746
ZL6-cust.ab1 149 T T 588
ZL6-cust.ab1 150 T C 199
ZL6-cust.ab1 151 C C 1021

peak ratio: 746+588 : 199+1021 = 1334 : 1220
Sample 7
File:SNP 7.png

Sample peak location base pair base pair peak value
ZL7-cust.ab1 197 A G 234
ZL7-cust.ab1 196 G G 476
ZL7-cust.ab1 197 A A 1358
ZL7-cust.ab1 198 A A 790


peak ratio: 234+476 : 1358+790 = 710 : 2148

The two samples we are really interested in are sample #6 and #7. The sample is GM20431 cDNA with rs 1264899 forward and reverse primer. The SNP location is rs 1264899. Then we will use software PeakPicker to compare and quantize the peaks.
Here is the files of the original sequencing result files: