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==Background== *Kun thinks the results from the experiment Noi did on Illumina’s plasma samples looks promising. *He thinks we should repeat the same experiments on all our cancer and plasma samples. *We should have all those WGBS libraries ready, so it would be just a BSPP capturing experiment (we might need to make more probes though). *Kun asked Noi to help me identify the reagents and design a capturing experiment on all WGBS libraries *Noi said she had already finished the BSPP capture on WGBS libraries and she will need my help to pool the libraries and do size selection *Noi will update her wiki so I can follow her work *Noi used 600ng of WGBS libraries for capture instead of the 400ng for illumina. *She reduced the probe to target ratio from 200:1 to 125:1due to limited amount of probes. *She also used MONOD V5A probe set (LMS cluster) and the rest of the protocol are pretty much the same. *She quantified the library concentration by PAGE quantification, there seems to be a little high variation between different gels *She asked me to do size selection of 6 pools (8 individual libraries each) of sequencing libraries as noted in her wiki. *I will have to cut the get in the range between 300-350bp (Do not of over 400bp) since she cropped the images to show me. *There will probably be high background over 400bp, and that is probably ssDNA form when she did more PCR cycles (should have done 1-2 cycle less) *Use one 5-well TBE gel per one pool of libraries *The individual sequencing libraries are in the PCR rack on the top shelf of -20C freezer as shown in the wiki. *Noi already filled in the sequencing spreadsheet *For Illumina experiment, Noi suggested Li to only pool sequencing libraries and re-purified with 0.7% AMPure beads to concentrate the libraries and remove the remaining primer dimers. *However, for Li libraries, I got low background of a smear over 400bp. http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2014-12-16#PAGE_size_selection_.26_Sequencing_library_information
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