AlanFung:LabNotes/Capturing/2012-8-10: Difference between revisions
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| align="center" | 1 | | align="center" | 1 | ||
| GM12878 | | GM12878 | ||
| align="center" | | | align="center" | 10 | ||
| align="center" | | | align="center" | | ||
| align="center" | | | align="center" | | ||
|- style="font-size:8pt" align="center" | |- style="font-size:8pt" align="center" | ||
| height="11" | 2X Kapa | | height="11" | 2X Kapa HiFi mix | ||
| align="center" | 50 | | align="center" | 50 | ||
| align="center" | 550 | | align="center" | 550 | ||
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| align="center" | 2 | | align="center" | 2 | ||
| H0 | | H0 | ||
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| H7 | | H7 | ||
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| H14 | | H14 | ||
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| H16 | | H16 | ||
| align="center" | | | align="center" | 9 | ||
| H16 | | H16 | ||
| align="center" | | | align="center" | 14 | ||
| align="center" | | |||
| align="center" | | |||
|- style="font-size:8pt" align="center" | |||
| height="11" | SYBR Green 50X | |||
| align="center" | 0.4 | |||
| align="center" | 4.4 | |||
| align="center" | | |||
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| align="center" | | | align="center" | | ||
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| Do not add to MM | | Do not add to MM | ||
| GM12878 | | GM12878 | ||
| align="center" | | | align="center" | 15 | ||
| GM | | GM | ||
| align="center" | | | align="center" | 22 | ||
| H7 | | H7 | ||
| align="center" | | | align="center" | 27 | ||
|- style="font-size:8pt" align="center" | |- style="font-size:8pt" align="center" | ||
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| align="center" | 825 | | align="center" | 825 | ||
| P10 | | P10 | ||
| align="center" | | | align="center" | 16 | ||
| H0 | | H0 | ||
| align="center" | | | align="center" | 23 | ||
| H14 | | H14 | ||
| align="center" | | | align="center" | 28 | ||
|- style="font-size:8pt" align="center" | |- style="font-size:8pt" align="center" | ||
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| align="center" | 66 | | align="center" | 66 | ||
| DF2 | | DF2 | ||
| align="center" | | | align="center" | 17 | ||
| H7 | | H7 | ||
| align="center" | | | align="center" | 24 | ||
| H16 | | H16 | ||
| align="center" | | | align="center" | 29 | ||
|- style="font-size:8pt" align="center" | |- style="font-size:8pt" align="center" | ||
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| Do not add to MM | | Do not add to MM | ||
| H0 | | H0 | ||
| align="center" | | | align="center" | 18 | ||
| H14 | | H14 | ||
| align="center" | | | align="center" | 25 | ||
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| align="center" | 511.5 | | align="center" | 511.5 | ||
| H7 | | H7 | ||
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| H16 | | H16 | ||
| align="center" | | | align="center" | 26 | ||
| align="center" | | | align="center" | | ||
| align="center" | | | align="center" | | ||
|- style="font-size:8pt" align="center" | |- style="font-size:8pt" align="center" | ||
| | | height="11" | SYBR Green 50X | ||
| align="center" | | | align="center" | 0.4 | ||
| align="center" | | | align="center" | 6.6 | ||
| H14 | | H14 | ||
| align="center" | | | align="center" | 20 | ||
| align="center" | | | align="center" | | ||
| align="center" | | | align="center" | | ||
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| H16 | | H16 | ||
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95C 2min -> (98C 20S -> 58C 20S -> 72C 20S) x 6 -> (98C 10S -> 72C 20S) x40 | |||
Monitor the reactions and terminate the program right before the amplification curves reach the plateau. | Monitor the reactions and terminate the program right before the amplification curves reach the plateau. | ||
==Indexing PCR for 3 samples== |
Latest revision as of 13:41, 18 August 2012
Capturing Remaining Gimelbrant lab Sample[edit]
- Add 2 drops of mineral oil to prevent evaporation
- Samples stored at tall -20C Alan Rack white box red label "Gimelbrant Lab"
ChIPK36me3 | Concentration ng/ul | Vol | Vol of probes | 10X Ampligase Buffer | H2O | Total |
GM12878 | 0.90 | 40.00 | 0.45 | 2 | 7.6 | 50 |
H0 | 1.00 | 40.00 | 0.50 | 2 | 7.5 | 50 |
H7 | 0.60 | 40.00 | 0.30 | 2 | 7.7 | 50 |
H14 | 0.50 | 40.00 | 0.25 | 2 | 7.8 | 50 |
H16 | 0.60 | 40.00 | 0.30 | 2 | 7.7 | 50 |
ChIPK27me3 | Concentration ng/ul | Vol | Vol of probes | 10X Ampligase Buffer | H2O | Total |
GM12878 | 1.20 | 40.00 | 0.60 | 2 | 7.4 | 50 |
H0 | 2.4 | 40.00 | 1.20 | 2 | 6.8 | 50 |
H7 | 1.2 | 40.00 | 0.60 | 2 | 7.4 | 50 |
H14 | 0.5 | 40.00 | 0.25 | 2 | 7.8 | 50 |
H16 | 1.3 | 40.00 | 0.65 | 2 | 7.4 | 50 |
WCE | Concentration ng/ul | Vol | Vol of probes | 10X Ampligase Buffer | H2O | Total |
GM12878 | 35.39 | 5.65 | 2.49 | 2 | 9.9 | 20 |
P10 | 35.39 | 5.65 | 2.49 | 2 | 9.9 | 20 |
DF2 | 35.39 | 5.65 | 2.49 | 2 | 9.9 | 20 |
H0 | 35.39 | 5.65 | 2.49 | 2 | 9.9 | 20 |
H7 | 35.39 | 5.65 | 2.49 | 2 | 9.9 | 20 |
H14 | 35.39 | 5.65 | 2.49 | 2 | 9.9 | 20 |
H16 | 35.39 | 5.65 | 2.49 | 2 | 9.9 | 20 |
cDNA | Concentration ng/ul | Vol | Vol of probes | 10X Ampligase Buffer | H2O | Total |
GM | 38.12 | 5.25 | 2.49 | 2 | 10.3 | 20 |
H0 | 38.12 | 5.25 | 2.49 | 2 | 10.3 | 20 |
H7 | 38.12 | 5.25 | 2.49 | 2 | 10.3 | 20 |
H14 | 38.12 | 5.25 | 2.49 | 2 | 10.3 | 20 |
H16 | 38.12 | 5.25 | 2.49 | 2 | 10.3 | 20 |
gDNA | Concentration ng/ul | Vol | Vol of probes | 10X Ampligase Buffer | H2O | Total |
H7 | 38.12 | 5.25 | 2.49 | 2 | 10.3 | 20 |
H14 | 38.12 | 5.25 | 2.49 | 2 | 10.3 | 20 |
H16 | 38.12 | 5.25 | 2.49 | 2 | 10.3 | 20 |
- When adding regents to the tube make sure you penetrate the oil layer
Store under βCES36K 95C 2min -> -0.2C/sec to 60C -> 60C 24h -> add 1ul/2.5ul(for 50ul rxn) SLN mix (dNTP 5uM, Stoffel 2U/ul, AmpLigase 1U/ul) -> 60C 18h -> 94C 1min -> 37c 1min -> add 2ul(5ul for 50ul rxn) Exo I&III -> 37C 2h -> 90C 5min -> 4C hold
Prepare SLN Mix[edit]
- Dilute 1mM dNTP 1 in 100 to 10uM dNTP
SLN Mix for 20ul Rxn | 1x | 16x |
dNTP (10uM) | 0.5 | 8 |
Stoffel (10U/ul) | 0.2 | 3.2 |
Ampligase (5U/ul) | 0.2 | 3.2 |
H2O | 0.1 | 1.6 |
SLN Mix for 50ul Rxn | 1x | 11x |
dNTP (10uM) | 1.25 | 13.75 |
Stoffel (10U/ul) | 0.5 | 5.5 |
Ampligase (5U/ul) | 0.5 | 5.5 |
H2O | 0.25 | 2.75 |
Prepare Exo I and Exo III Mix[edit]
Exo I & III for 20ul Rxn | 1X | 16x |
Exo I (20U/ul) | 1 | 16 |
ExoIII (200U/ul) | 1 | 16 |
Exo I & III for 50ul Rxn | 1X | 11x |
Exo I (20U/ul) | 2.5 | 6.25 |
ExoIII (200U/ul) | 2.5 | 6.25 |
Indexing qPCR[edit]
- Perform one step qPCR using Indexing seq. primer
Content (50ul Capture) 4 rxn | Volume | Master Mix | ChIPK36me3 | Index | ChIPK27me3 | Index | ||
Captured DNA | 27 | Do not add to MM | GM12878 | 1 | GM12878 | 10 | ||
2X Kapa HiFi mix | 50 | 550 | H0 | 2 | H0 | 11 | ||
10uM AmpF6.3Sol | 4 | 44 | H7 | 3 | H7 | 12 | ||
10uM AmpR6.3Ind | 4 | Do not add to MM | H14 | 4 | H14 | 13 | ||
H2O | 15 | 165 | H16 | 9 | H16 | 14 | ||
SYBR Green 50X | 0.4 | 4.4 | ||||||
Content (20ul Capture) 7rxn | Volume | Master Mix | WCE | Index | cDNA | Index | gDNA | Index |
Captured DNA | 11 | Do not add to MM | GM12878 | 15 | GM | 22 | H7 | 27 |
2X Kapa SYBG qPCR master mix | 50 | 825 | P10 | 16 | H0 | 23 | H14 | 28 |
10uM AmpF6.3Sol | 4 | 66 | DF2 | 17 | H7 | 24 | H16 | 29 |
10uM AmpR6.3Ind | 4 | Do not add to MM | H0 | 18 | H14 | 25 | ||
H2O | 31 | 511.5 | H7 | 19 | H16 | 26 | ||
SYBR Green 50X | 0.4 | 6.6 | H14 | 20 | ||||
H16 | 21 |
95C 2min -> (98C 20S -> 58C 20S -> 72C 20S) x 6 -> (98C 10S -> 72C 20S) x40 Monitor the reactions and terminate the program right before the amplification curves reach the plateau.