Noi/NOTES/2014-3-19: Difference between revisions

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= Experimental plan to test sensitivity of BSPP capture =
= Experimental plan to test sensitivity of BSPP capture =
* In the future we want to apply BSPP to capture circulating DNA which are fragmented DNA and total amount for capture is very low. Therefore Dr. Zhang wanted to test the sensitivity of BSPP capture at different bisulfite converted DNA amount. At the same time, he wanted to improve the sensitivity of BSPP capture by performing low magnitude amplification with N9 primer and another option is doing multiple rounds of heat denaturation at 98C and circularization at 55C (I'll look into more details in previous published papers.).
* In the future, we want to apply BSPP to capture circulating DNA which are fragmented DNA and total amount for capture is very low. Therefore Dr. Zhang wanted to test the sensitivity of BSPP capture at different bisulfite converted DNA amount. At the same time, he wanted to improve the sensitivity of BSPP capture by performing low magnitude amplification with N9 primer and another option is doing multiple rounds of heat denaturation at 98C and circularization at 55C (I'll look into more details in previous published papers.).
* The sensitivity could be varied depends on the size of probe set and efficiency of BSPP as well. In this experiment, he wanted to use MONOD GP1_V4 probe set that is not too big (7,110 probes) and had been tested in previous experiment.
* The sensitivity could be varied depends on the size of probe set and efficiency of BSPP as well. In this experiment, he wanted to use MONOD GP1_V4 probe set that is not too big (7,110 probes) and had been tested in previous experiment.
* I will be addressing the experiment to test HOTSPOTS 460k probe set later since I need to use this probe set to capture BSC samples from Illumina if the capture by this probe set work well. Otherwise, I will be using MONOD GP1 to capture BSC samples.
* I will be addressing the experiment to test HOTSPOTS 460k probe set later since I need to use this probe set to capture BSC samples from Illumina if the capture by this probe set work well. Otherwise, I will be using MONOD GP1 to capture BSC samples.

Revision as of 04:01, 20 March 2014

Experimental plan to test sensitivity of BSPP capture

  • In the future, we want to apply BSPP to capture circulating DNA which are fragmented DNA and total amount for capture is very low. Therefore Dr. Zhang wanted to test the sensitivity of BSPP capture at different bisulfite converted DNA amount. At the same time, he wanted to improve the sensitivity of BSPP capture by performing low magnitude amplification with N9 primer and another option is doing multiple rounds of heat denaturation at 98C and circularization at 55C (I'll look into more details in previous published papers.).
  • The sensitivity could be varied depends on the size of probe set and efficiency of BSPP as well. In this experiment, he wanted to use MONOD GP1_V4 probe set that is not too big (7,110 probes) and had been tested in previous experiment.
  • I will be addressing the experiment to test HOTSPOTS 460k probe set later since I need to use this probe set to capture BSC samples from Illumina if the capture by this probe set work well. Otherwise, I will be using MONOD GP1 to capture BSC samples.
  • Since we’re pretty sure that 100-300ng work fine for capture, I am doing additional experiment to improve sensitivity of BSPP capture for the low input (<100ng).
Summary Table:
File:MONOD-sensitivity-test-plans.png
  • I will add more details of this experimental plan and ask Dr. Zhang's opinion if he agrees with this plan