Kun Zhang LabNote Oct week2: Difference between revisions
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== | ==Friday 2007-10-12== | ||
=== | ===Fri.Exp1: Repeat: PCR on PGP1 and Hues6 gDNA/cDNA for Sanger sequencing=== | ||
Summary of reactions: | Summary of reactions: | ||
{| {{table}} | {| {{table}} | ||
Line 71: | Line 71: | ||
95C 3min -> 35 cycles of (95C 15S -> 58C 30S -> 72C 1min) -> 72C 3min <br> | 95C 3min -> 35 cycles of (95C 15S -> 58C 30S -> 72C 1min) -> 72C 3min <br> | ||
===Fri.Exp2: Set up PCR using the PGP1VER2 primer set=== | |||
cDNA primers on the plate | |||
{| border="1" cellspacing="0" {{table}} | |||
| colspan="4" align="center" style="background:#f0f0f0;"|'''Forward primer''' | |||
| colspan="4" align="center" style="background:#f0f0f0;"|'''Reverse primer''' | |||
| colspan="4" align="center" style="background:#f0f0f0;"|'''Seq. Primer''' | |||
|- | |||
| A1||A2||A3||A4||A5||A6||A7||A8||A9||A10||A11||A12 | |||
|- | |||
| B1||B2||B3||B4||B5||B6||B7||B8||B9||B10||B11||B12 | |||
|- | |||
| C1||C2||C3||C4||C5||C6||C7||C8||C9||C10||C11||C12 | |||
|- | |||
| D1||D2||D3||D4||D5||D6||D7||D8||D9||D10||D11||D12 | |||
|- | |||
| E1||E2||E3||E4||E5||E6||E7||E8||E9||E10||E11||E12 | |||
|- | |||
| F1||F2||F3||F4||F5||F6||F7||F8||F9||F10||F11||F12 | |||
|- | |||
| G1||G2||G3||G4||G5||G6||G7||G8||G9||G10||G11||G12 | |||
|- | |||
| H1||H2||H3||H4||H5||H6||H7||H8||H9||H10||H11||H12 | |||
|} | |||
gDNA primers on the plate: | |||
{| border="1" cellspacing="0" {{table}} | |||
| colspan="4" align="center" style="background:#f0f0f0;"|'''Forward primer''' | |||
| colspan="4" align="center" style="background:#f0f0f0;"|'''Reverse primer''' | |||
| colspan="4" align="center" style="background:#f0f0f0;"|'''Seq. Primer''' | |||
|- | |||
| A1||A2||||A4||A5||A6||||A8||A9||A10||||A12 | |||
|- | |||
| B1||||||B4||B5||||||B8||B9||||||B12 | |||
|- | |||
| C1||C2||C3||||C5||C6||C7||||C9||C10||C11|| | |||
|- | |||
| ||D2||D3||||||D6||D7||||||D10||D11|| | |||
|- | |||
| ||E2||E3||E4||||E6||E7||E8||||E10||E11||E12 | |||
|- | |||
| F1||||F3||F4||F5||||F7||F8||F9||||F11||F12 | |||
|- | |||
| G1||||G3||G4||G5||||G7||G8||G9||||G11||G12 | |||
|- | |||
| H1||H2||H3||||H5||H6||H7||||H9||H10||H11|| | |||
|} |
Revision as of 07:26, 12 October 2007
Friday 2007-10-12
Fri.Exp1: Repeat: PCR on PGP1 and Hues6 gDNA/cDNA for Sanger sequencing
Summary of reactions:
Reaction | SNP | PCR primer | Primer location | Sample |
1(1A) | rs3753565 | rs3753565_F/rs3753565_R | SnpVer2 A1/A12 | Hues6 gDNA |
2(1B) | rs3753565 | rs3753565_F/rs3753565_R | SnpVer2 A1/A12 | Hues6 cDNA |
3(1C) | rs2295680 | rs2295680_F/rs2295680_R | SnpVer2 A2/B1 | PGP1 gDNA |
4(1D) | rs2295680 | rs2295680_F/rs2295680_R | SnpVer2 A2/B1 | GM20431 cDNA |
5(1E) | rs2295680 | rs2295680_F/rs2295680_R | SnpVer2 A2/B1 | GC1F cDNA |
6(1F) | rs2295680 | rs2295680_F/rs2295680_R | SnpVer2 A2/B1 | GC1EP cDNA |
7(1G) | rs6103 | rs6103_F/rs6103_R | SnpVer2 A9/B8 | PGP1 gDNA |
8(1H) | rs6103 | rs6103_F/rs6103_R | SnpVer2 A9/B8 | GM20431 cDNA |
9(2A) | rs6103 | rs6103_F/rs6103_R | SnpVer2 A9/B8 | GC1F cDNA |
10(2B) | rs6103 | rs6103_F/rs6103_R | SnpVer2 A9/B8 | GC1EP cDNA |
11(2C) | rs6103 | rs6103_F/rs6103_R | SnpVer2 A9/B8 | Hues6 gDNA |
12(2D) | rs6103 | rs6103_F/rs6103_R | SnpVer2 A9/B8 | Hues6 cDNA |
13(2E) | rs1264899 | rs1264899_cF/rs1264899_cR | Hues6Ver2c F1/F4 | PGP1 gDNA |
14(2F) | rs1264899 | rs1264899_cF/rs1264899_cR | Hues6Ver2c F1/F4 | GM20431 cDNA |
15(2G) | rs1264899 | rs1264899_cF/rs1264899_cR | Hues6Ver2c F1/F4 | GC1F cDNA |
16(2H) | rs1264899 | rs1264899_cF/rs1264899_cR | Hues6Ver2c F1/F4 | GC1EP cDNA |
Template: 10ng genomic DNA or 2ng cDNA, use new aliquots of templates/primers/SYBG I diluted in nuclease free H2O.
' | one reaction | total |
Template | 1 | 17 |
10x Buffer | 5 | 85 |
50mM MgCl2 | 1.5 | 25.5 |
10mM dNTP | 1 | 17 |
10uM forward primer | 1 | 17 |
10uM reverse primer | 1 | 17 |
50x SYBG I | 0.4 | 6.8 |
iTaq | 0.25 | 4.25 |
H2O | 38.85 | 660.45 |
95C 3min -> 35 cycles of (95C 15S -> 58C 30S -> 72C 1min) -> 72C 3min
Fri.Exp2: Set up PCR using the PGP1VER2 primer set
cDNA primers on the plate
Forward primer | Reverse primer | Seq. Primer | |||||||||
A1 | A2 | A3 | A4 | A5 | A6 | A7 | A8 | A9 | A10 | A11 | A12 |
B1 | B2 | B3 | B4 | B5 | B6 | B7 | B8 | B9 | B10 | B11 | B12 |
C1 | C2 | C3 | C4 | C5 | C6 | C7 | C8 | C9 | C10 | C11 | C12 |
D1 | D2 | D3 | D4 | D5 | D6 | D7 | D8 | D9 | D10 | D11 | D12 |
E1 | E2 | E3 | E4 | E5 | E6 | E7 | E8 | E9 | E10 | E11 | E12 |
F1 | F2 | F3 | F4 | F5 | F6 | F7 | F8 | F9 | F10 | F11 | F12 |
G1 | G2 | G3 | G4 | G5 | G6 | G7 | G8 | G9 | G10 | G11 | G12 |
H1 | H2 | H3 | H4 | H5 | H6 | H7 | H8 | H9 | H10 | H11 | H12 |
gDNA primers on the plate:
Forward primer | Reverse primer | Seq. Primer | |||||||||
A1 | A2 | A4 | A5 | A6 | A8 | A9 | A10 | A12 | |||
B1 | B4 | B5 | B8 | B9 | B12 | ||||||
C1 | C2 | C3 | C5 | C6 | C7 | C9 | C10 | C11 | |||
D2 | D3 | D6 | D7 | D10 | D11 | ||||||
E2 | E3 | E4 | E6 | E7 | E8 | E10 | E11 | E12 | |||
F1 | F3 | F4 | F5 | F7 | F8 | F9 | F11 | F12 | |||
G1 | G3 | G4 | G5 | G7 | G8 | G9 | G11 | G12 | |||
H1 | H2 | H3 | H5 | H6 | H7 | H9 | H10 | H11 |