AlanFung:LabNotes/Capturing/BisFirstExon 2009 12 4: Difference between revisions
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Step7 4C, Forever | Step7 4C, Forever | ||
==TBE Gel Verification== | ==TBE Gel Verification== | ||
*Run 3 10 well gels | |||
Gel 1 | |||
Ladder NA12878(22) NA12878(21) NA12878(8) NA18507(22) NA18507(21) NA18507(8) NA20431(22) NA20431(21) NA20431(8) | |||
Gel 2 | |||
Ladder CV-Fibr(22) CV-Fibr(21) CV-Fibr(8) CV-iPSB(22) CV-iPSB(21) CV-iPSB(8) CV-iPSF(22) CV-iPSF(21) CV-iPSF(8) | |||
Gel 3 |
Revision as of 00:21, 5 December 2009
qPCR Validation(3 Bisulfite Conversion Primers)
- Start with 10ng template for each set of primer (30ng Total)
Sample | Sample Concentration ng/ul | To get 30ng | 1/10 Dilution | To get 30ng |
NA12878 | 17.6 | 1.7 | ||
NA18507 | 12.4 | 2.42 | ||
NA20431 | 50.6 | 0.59 | ||
CV-Fibr | 4.84 | 6.2 | ||
CV-iPS-B | 7.27 | 4.13 | ||
CV-iPS-F | 6.91 | 4.34 | ||
Jurkat | 55.4 | 0.54 | 5.54 | 5.42 |
Jurkat (old) | 104 | 0.29 | 10.4 | 2.88 |
- Mix 50/50 old/new Jurkat to make up 30ng
New: 2.71ul Old: 1.44ul
Sample | Volume | Make it up to 24ul |
NA12878 | 1.7 | 22.3 |
NA18507 | 2.42 | 21.58 |
NA20431 | 0.59 | 23.41 |
CV-Fibr | 6.2 | 17.8 |
CV-iPS-B | 4.13 | 19.87 |
CV-iPS-F | 4.34 | 19.66 |
Jurkat | 5.42 | 18.58 |
Jurkat (old) | 2.88 | 21.12 |
Jurkat (mix) | (NEW)2.71+(OLD)1.44 | 19.85 |
Prepare Master Mix
X1.05 | CHR22 | CHR21 | CHR8 |
2X iQ Super Mix | 189 | 189 | 189 |
Primer F (3.3uM) | 56.7 | 56.7 | 56.7 |
Primer R (3.3uM) | 56.7 | 56.7 | 56.7 |
- Aliquot 32ul to each well +8ul sample =40ul Total
Perform PCR reaction in real-time thermocycler
CHR22 | CHR21 | CHR8 | |
NA12878 | NA12878 | NA12878 | Jurkat (mix) CHR22 |
NA18507 | NA18507 | NA18507 | Jurkat (mix) CHR21 |
NA20431 | NA20431 | NA20431 | Jurkat (mix) CHR8 |
CV-Fibr | CV-Fibr | CV-Fibr | |
CV-iPS-B | CV-iPS-B | CV-iPS-B | |
CV-iPS-F | CV-iPS-F | CV-iPS-F | |
Jurkat | Jurkat | Jurkat | |
Jurkat (old) | Jurkat (old) | Jurkat (old) | |
Step1 96C, 3m Step2 95C, 30s Step3 62C, 1m Step4 72C, 1m Step5 Go to step2 repeat 39 times Step6 72C, 5m Step7 4C, Forever
TBE Gel Verification
- Run 3 10 well gels
Gel 1 Ladder NA12878(22) NA12878(21) NA12878(8) NA18507(22) NA18507(21) NA18507(8) NA20431(22) NA20431(21) NA20431(8)
Gel 2 Ladder CV-Fibr(22) CV-Fibr(21) CV-Fibr(8) CV-iPSB(22) CV-iPSB(21) CV-iPSB(8) CV-iPSF(22) CV-iPSF(21) CV-iPSF(8)
Gel 3