Jie:LabNotes/CpgSeq/2009-5-29: Difference between revisions
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*Measure the DNA with Nanodrop: | *Measure the DNA with Nanodrop: | ||
RNA | RNA | ||
==set up the capture reaction== | |||
{| border="1" cellpadding="5" cellspacing="0" align="center" | |||
|- | |||
| align="center" style="background:#f0f0f0;"|'''No ''' | |||
| align="center" style="background:#f0f0f0;"|'''sample ''' | |||
|align="center" style="background:#f0f0f0;"|'''sample concentration''' | |||
| align="center" style="background:#f0f0f0;"|'''10xLigase buffer''' | |||
| align="center" style="background:#f0f0f0;"|'''template+cpg30k(10ng/ul,2009-05-29 by Alan)+suppressor(8nM each)vol+H2O''' | |||
| align="center" style="background:#f0f0f0;"|'''template+v2.1(21ng/ul) vol+H2O''' | |||
| align="center" style="background:#f0f0f0;"|'''template+v2.2(21ng/ul) vol+H2O''' | |||
| align="center" style="background:#f0f0f0;"|'''template+v2.3(20ng/ul) vol+H2O''' | |||
| align="center" style="background:#f0f0f0;"|'''template+Jan09#2 vol+H2O''' | |||
|- | |||
|09_8||DF6-9-9_P16(4)||285.7ng/ul x 10ul||1ul||1+3+1+3ul||1+1.5+6.5||3+1.5+4.5||2+1.5+5.5||2+ | |||
|- | |||
|09_9||foreskin||212.5ng/ul x 10ul||1ul||1+1+1+6ul||1+1.5+6.5||3+1.5+4.5||2+1.5+5.5 | |||
|- | |||
| ||positive control||200ng/ul||1ul||1+1+1+6ul||1+1.5+6.5||3+1.5+4.5||2+1.5+5.5 | |||
|- | |||
| ||negative control||0||1ul||1+1+1+6ul||1+1.5+6.5||3+1.5+4.5||2+1.5+5.5 | |||
|} |
Revision as of 22:04, 29 May 2009
Bisulfite conversion of PGP DNA for cpg30k ASM validation
No | sample | sample concentration | sample volumn | ddH2O | conversion reagents | conversed DNA concentration and volumn |
20 | GM20431 | 256ng/ul x 1 tube | 8ul | 12ul | 130ul | 56.1ng/ul x 10ul |
21 | PGP1_iPS1 | 50ng/ul x 1 tubes | 10ul | 10ul | 130ul | 40.7ng/ul x 10ul |
22 | PGP1_L | 293ng/ul x 1 tubes | 6.8ul | 13.2ul | 130ul | 191.6ng/ul x 10ul |
23 | PGP3_L | 242ng/ul x 1 tubes | 6.8ul | 13.2ul | 130ul | 114.7ng/ul x 10ul |
24 | PGP9_L | 249ng/ul x 1 tubes | 6.8ul | 13.2ul | 130ul | 106.5ng/ul x 10ul |
09_8 | DF6-9-9_P16(4) | 504.8ng/ul x 3 tubes | 4ul | 16ul | 130ul | 285.7ng/ul x 10ul |
09_9 | foreskin | 583ng/ul x 2 tube | 4ul | 16ul | 130ul | 212.5ng/ul x 10ul |
- Add 900ul ddH2O, 300ul M-Dilution Buffer and 50ul M-Dissolving Buffer to a tube of CT Conversion Reagent.
- Add 130ul of CT conversion reagent to samples.
- 98C 10min -> 64C 150min -> 4c overnight.
- Add 600ul M-Binding buffer to spin columns.
- Add the converted samples to the columns, close the gap and mix by inverting several times.
- Spin at 15,000rpm for 30sec.
- Add 100ul M-Wash Buffer, spin for 30 sec, discard flow-through.
- Add 200ul M-Desulphonation Buffer, wait for 20min, spin at 15,000 rpm for 30sec.
- Add 200ul M-Wash Buffer, spin for 30 sec.
- Place the columns into 1.5ml tubes, add 10ul M-Elution Buffer. Wait for 1min, spin at 15,000rpm for 30sec.
- Measure the DNA with Nanodrop:
RNA
set up the capture reaction
No | sample | sample concentration | 10xLigase buffer | template+cpg30k(10ng/ul,2009-05-29 by Alan)+suppressor(8nM each)vol+H2O | template+v2.1(21ng/ul) vol+H2O | template+v2.2(21ng/ul) vol+H2O | template+v2.3(20ng/ul) vol+H2O | template+Jan09#2 vol+H2O |
09_8 | DF6-9-9_P16(4) | 285.7ng/ul x 10ul | 1ul | 1+3+1+3ul | 1+1.5+6.5 | 3+1.5+4.5 | 2+1.5+5.5 | 2+ |
09_9 | foreskin | 212.5ng/ul x 10ul | 1ul | 1+1+1+6ul | 1+1.5+6.5 | 3+1.5+4.5 | 2+1.5+5.5 | |
positive control | 200ng/ul | 1ul | 1+1+1+6ul | 1+1.5+6.5 | 3+1.5+4.5 | 2+1.5+5.5 | ||
negative control | 0 | 1ul | 1+1+1+6ul | 1+1.5+6.5 | 3+1.5+4.5 | 2+1.5+5.5 |