Noi:LabNotes/2010-10-21: Difference between revisions
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'''DMR220k_S4''' | '''DMR220k_S4''' '''DMR220k_S5''' | ||
Single-strand(SS) amplicon conc. (ng/ul) 81.3 75.9 | Single-strand(SS) amplicon conc. (ng/ul) 81.3 75.9 | ||
O.D.260/280 1.96 1.96 | O.D.260/280 1.96 1.96 | ||
Yield: conc. x total vol. 81.3ng/ulx240ul = 19.5ug 75.9ng/ulx240ul = 18.2ug | Yield: conc. x total vol. 81.3ng/ulx240ul = 19.5ug 75.9ng/ulx240ul = 18.2ug | ||
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===Removal of amplification adaptors=== | ===Removal of amplification adaptors=== | ||
'''DMR220k_S4''' | '''DMR220k_S4''' '''DMR220k_S5''' | ||
ss-amplicon 75ul (6.1ug) 75ul (5.7ug) | ss-amplicon 75ul (6.1ug) 75ul (5.7ug) | ||
USER 5ul 5ul | USER 5ul 5ul | ||
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- Each eluted with 60ul EB (total vol: 4 x 60 = 240ul) | - Each eluted with 60ul EB (total vol: 4 x 60 = 240ul) | ||
'''DMR220k_S4''' '''DMR220k_S5''' | |||
USER/DpnII digested DNA conc. (ng/ul) | QQ purified USER/DpnII digested DNA conc.(ng/ul) | ||
O.D.260/280 | 44.5 40.0 | ||
Yield: conc. x total vol. | O.D.260/280 1.99 1.96 | ||
Yield: conc. x total vol. 44.5ng/ulx240ul = 10.7ug 40.0ng/ulx240ul = 9.6ug |
Revision as of 02:13, 24 October 2010
Probe prep for the DMR220k S4 and S5
(followed Dr. Zhang's conditions)
Production PCR
98rxn mix 10nM 1st round amplicon 0.2ul 19.6ul 2x Kapa SYBG qPCR Master Mix 50ul 4900ul 100uM pAP1V61U 0.4ul 39.2ul 100uM AP2V6 0.4ul 39.2ul H2O 49ul 4802ul =================================== 100ul x 96
95C 30sec (95C 3sec -> 55C 30sec-> 60C 20sec) x 15 cycles 60C 2min 15C hold. - Ethanol precipitation - Re-purified with twelve Qiaquick columns - Each eluted with 41ul EB (total vol: 12 x 41 = 492ul).
DMR220k_S4 DMR220k_S5 Amplified amplicon conc. (ng/ul) 194.2 192.7 O.D.260/280 1.93 1.92 Yield: conc. x total vol. 194.2ng/ulx492ul= 95.5ug 192.7ng/ulx492ul = 94.8ug
Lambda exo digestion
DMR220k_S4 DMR220k_S5 Qiaquick (QQ)amplified amplicon 108ul (21.0ug) 108ul (20.8ug) 10x Lambda Exo buffer 15ul 15ul Lambda exo 10ul 10ul H20 17ul 17ul ----------------------------------------------------- Total 100ul x 4.5 100ul x 4.5 Total amount of QQ amplified amplicon 94.4ug 93.6ug - 37C 1h - Purified with four Qiaquick columns - Each eluted with 60ul EB (total vol: 4 x 60 = 240ul)
DMR220k_S4 DMR220k_S5 Single-strand(SS) amplicon conc. (ng/ul) 81.3 75.9 O.D.260/280 1.96 1.96 Yield: conc. x total vol. 81.3ng/ulx240ul = 19.5ug 75.9ng/ulx240ul = 18.2ug
Removal of amplification adaptors
DMR220k_S4 DMR220k_S5 ss-amplicon 75ul (6.1ug) 75ul (5.7ug) USER 5ul 5ul ----------------------------------------------------- Total 80ul x 3 80ul x 3 Total amount of ss amplicon 18.3ug 17.1ug - 37C 1hr - Add prepare rxn mix for 6.1x 10x DpnII buffer 10ul 10ul 61ul 100uM RE-DpnII-V66 guide oligo 5ul 5ul 30.5ul - 94C 2min, 37C 3min - mix and aliquot 15ul to each tube - Add DpnII 5ul 5 ul - 37C 3hr - Add prepare rxn mix for 6.1x USER 5ul 5ul 30.5ul 10x DpnII buffer 10ul 10ul 61ul H2O 85ul 85ul 518.5ul - 37C O/N - mix and aliquot 100ul to each tube - 75C 20min
- Purified with four Qiaquick columns - Each eluted with 60ul EB (total vol: 4 x 60 = 240ul)
DMR220k_S4 DMR220k_S5 QQ purified USER/DpnII digested DNA conc.(ng/ul) 44.5 40.0 O.D.260/280 1.99 1.96 Yield: conc. x total vol. 44.5ng/ulx240ul = 10.7ug 40.0ng/ulx240ul = 9.6ug