Jie:LabNotes/CpgSeq/2008-7-31: Difference between revisions
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>Jie deng (New page: ==step2. Digestion with MmeI== dUTP 250uM,167.3ng/ul dUTP 100uM, 159.8ng/ul (06/17/2008) Total 20ul DNA ...) |
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==sequencing library construction== | |||
==2nd PCR amplification with AmpF6.3/AmpR6.3 and dUTP:dNTP 1:40 == | |||
reaction system x4 x3 | |||
H2O 43.2ul 172.8ul 518.4 | |||
2x Master mix 50ul 200ul 600 | |||
dUTP(1mM) 2ul 8ul 24 | |||
AmpF6.3(10uM) 2ul 8ul 24 | |||
AmpR6.3(10uM) 2ul 8ul 24 | |||
50x SYBG I 0.4ul 1.6ul 4.8 | |||
template(18.4ng/ul) 0.1ul 0.4ul 1.2 | |||
Total 100ul 400ul 2400 | |||
94C 3min -> 13cycles of (94C 45sec -> 55C 45sec -> 72C 45sec) -> 72C 3min -> 4C | |||
Bioneer column purification. Yield:167ng/ul x60ul | |||
==step2. Digestion with MmeI== | ==step2. Digestion with MmeI== | ||
dUTP 250uM,167.3ng/ul | dUTP 250uM,167.3ng/ul x2 | ||
Total 20ul | Total 20ul | ||
DNA 6ul | DNA 6ul 12 | ||
10X NEBuffer 4 2ul | 10X NEBuffer 4 2ul 4 | ||
1mM SAM(fresh) 2ul | 1mM SAM(fresh) 2ul 4 | ||
2U/ul Mme I 8ul | 2U/ul Mme I 8ul 16 | ||
ddH2O 2ul | ddH2O 2ul 4 | ||
1mM SAM: 32mM SAM 1ul + 31ul ddH2O. | 1mM SAM: 32mM SAM 1ul + 31ul ddH2O. | ||
37C 2h | 37C 2h | ||
MinElute column purify. Elute in | MinElute column purify. Elute in 22ul EB. | ||
[[Image:20080801_after MmeI.jpg]]20080801_after MmeI | |||
==step3. USER digestion== | ==step3. USER digestion== | ||
x2 | |||
DNA 10ul | DNA 10ul 20ul | ||
USER 3ul | USER 3ul 6ul | ||
total 13ul | total 13ul | ||
Line 29: | Line 49: | ||
37C 10mins. | 37C 10mins. | ||
Minelute cloumn purify. Elute in 18ul H2O. | Minelute cloumn purify. Elute in 18ul H2O. | ||
[[Image:20080801_after USER and S1.jpg]]20080801_after USER and S1 | |||
==step5. end repair== | ==step5. end repair== | ||
positive control | |||
Total 25ul | Total 25ul H2O 13ul | ||
DNA | DNA 15ul 2ul(20080801_spacer_107bp) | ||
dNTP 2.5ul | dNTP 2.5ul 2.5ul | ||
dATP 2.5ul | dATP 2.5ul 2.5ul | ||
10xendrepair buffer 2.5ul | 10xendrepair buffer 2.5ul 2.5ul | ||
enzyme 0.5ul | enzyme 0.5ul 0.5ul | ||
extra ATP(10mM) 2.5ul 2.5ul | |||
Keep at room temperature (~25C) for 45 minutes. Purify with Minelute. Elute in 14ul H2O. | Keep at room temperature (~25C) for 45 minutes. Purify with Minelute. Elute in 14ul H2O. | ||
==step6. adapter ligation== | ==step6. adapter ligation== | ||
total 30ul | total 30ul positive control negative control | ||
DNA 13ul | DNA 13ul 13ul ddH2O 13ul | ||
100uM Solexa_1 adaptor 0.5ul 0.5ul | 100uM Solexa_1 adaptor 0.5ul 0.5ul 0.5ul | ||
100uM Solexa_2 adaptor 0.5ul 0.5ul | 100uM Solexa_2 adaptor 0.5ul 0.5ul 0.5ul | ||
2xQuickLiage buffer 15ul 15ul | 2xQuickLiage buffer 15ul 15ul 15ul | ||
QuickLigase enzyme(NEB) 1ul 1ul | QuickLigase enzyme(NEB) 1ul 1ul 1ul | ||
extra ATP(10mM) 2.5ul 2.5ul 2.5ul | |||
Keep at room temperature (~25C) for 10 minutes. Purify with Minelute cilumn. Elute in 20ul H2O. | |||
[[Image: 20080801_after endrepair and ligation.jpg]] | |||
PAGE selection 150-175bp. Ethanol precipitation. Elute in 15ul ddH2O. | PAGE selection 150-175bp. Ethanol precipitation. Elute in 15ul ddH2O. | ||
==step7. Nick-translation== | ==step7. Nick-translation== | ||
Line 74: | Line 96: | ||
x3 | x3 | ||
Nick-translated DNA 10ul | Nick-translated DNA 10ul | ||
Solexa_PCR_up(10uM) | Solexa_PCR_up(10uM) 2ul 6ul | ||
Solexa_PCR_lo(10uM) | Solexa_PCR_lo(10uM) 2ul 6ul | ||
2xiProof master mix | 2xiProof master mix 50ul 150ul | ||
50x SYBG 0. | 50x SYBG 0.8ul 2.4ul | ||
ddH2O | ddH2O 35.2ul 106.6ul | ||
98C 30sec -> | 98C 30sec -> 12 cycles of (98C 10sec -> 65C 20 sec -> 72C 20sec) -> 72C 3min ->15C hold. | ||
[[Image:20080803_sequencing library.jpg]]20080803_sequencing library | |||
Purify with Qiaquick column. Elute in 30ul EB. | Purify with Qiaquick column. Elute in 30ul EB. | ||
yield: 22.9ng/ul(173nM) | |||
Latest revision as of 16:57, 4 August 2008
sequencing library construction[edit]
2nd PCR amplification with AmpF6.3/AmpR6.3 and dUTP:dNTP 1:40[edit]
reaction system x4 x3 H2O 43.2ul 172.8ul 518.4 2x Master mix 50ul 200ul 600 dUTP(1mM) 2ul 8ul 24 AmpF6.3(10uM) 2ul 8ul 24 AmpR6.3(10uM) 2ul 8ul 24 50x SYBG I 0.4ul 1.6ul 4.8 template(18.4ng/ul) 0.1ul 0.4ul 1.2 Total 100ul 400ul 2400
94C 3min -> 13cycles of (94C 45sec -> 55C 45sec -> 72C 45sec) -> 72C 3min -> 4C Bioneer column purification. Yield:167ng/ul x60ul
step2. Digestion with MmeI[edit]
dUTP 250uM,167.3ng/ul x2 Total 20ul DNA 6ul 12 10X NEBuffer 4 2ul 4 1mM SAM(fresh) 2ul 4 2U/ul Mme I 8ul 16 ddH2O 2ul 4 1mM SAM: 32mM SAM 1ul + 31ul ddH2O. 37C 2h MinElute column purify. Elute in 22ul EB.
File:20080801 after MmeI.jpg20080801_after MmeI
step3. USER digestion[edit]
x2 DNA 10ul 20ul USER 3ul 6ul total 13ul
37C 12h.
step4. S1 nuclease digestion[edit]
x2 10 x S1 nuclease buffer: 2ul 4ul DNA after USER digestion: 13ul 26ul S1 nuclease (10U/ul): 1ul 2ul ddH2O 4ul 8ul
37C 10mins. Minelute cloumn purify. Elute in 18ul H2O.
File:20080801 after USER and S1.jpg20080801_after USER and S1
step5. end repair[edit]
positive control Total 25ul H2O 13ul DNA 15ul 2ul(20080801_spacer_107bp) dNTP 2.5ul 2.5ul dATP 2.5ul 2.5ul 10xendrepair buffer 2.5ul 2.5ul enzyme 0.5ul 0.5ul extra ATP(10mM) 2.5ul 2.5ul
Keep at room temperature (~25C) for 45 minutes. Purify with Minelute. Elute in 14ul H2O.
step6. adapter ligation[edit]
total 30ul positive control negative control DNA 13ul 13ul ddH2O 13ul 100uM Solexa_1 adaptor 0.5ul 0.5ul 0.5ul 100uM Solexa_2 adaptor 0.5ul 0.5ul 0.5ul 2xQuickLiage buffer 15ul 15ul 15ul QuickLigase enzyme(NEB) 1ul 1ul 1ul extra ATP(10mM) 2.5ul 2.5ul 2.5ul
Keep at room temperature (~25C) for 10 minutes. Purify with Minelute cilumn. Elute in 20ul H2O.
File:20080801 after endrepair and ligation.jpg
PAGE selection 150-175bp. Ethanol precipitation. Elute in 15ul ddH2O.
step7. Nick-translation[edit]
set up the ligation system:
Total 20ul DNA 15ul 10x ThermoPol buffer 2ul 10mM dNTP 0.4ul 1mg/ml BSA 2ul Bst polymerase(8U/ul) 1ul
65C for 25 minutes -> keep on ice.
step8. PCR of sequencig library[edit]
x3 Nick-translated DNA 10ul Solexa_PCR_up(10uM) 2ul 6ul Solexa_PCR_lo(10uM) 2ul 6ul 2xiProof master mix 50ul 150ul 50x SYBG 0.8ul 2.4ul ddH2O 35.2ul 106.6ul 98C 30sec -> 12 cycles of (98C 10sec -> 65C 20 sec -> 72C 20sec) -> 72C 3min ->15C hold.
File:20080803 sequencing library.jpg20080803_sequencing library
Purify with Qiaquick column. Elute in 30ul EB. yield: 22.9ng/ul(173nM)