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= Measurement of the size distribution of WGBS libraries generated from cfDNA = [[noi:DMR220k_LabNotes|'''Link to calendar''']] * To verify the size distribution of wGBS libraries generated from cfDNA from plasma samples, I will ask Richard in Palsson's lab to run bioanalyzer. I might include cfDNA for some samples with a high yield (>10ng) to compare. * Things to do: List samples to be included for Bioanalyzer ** WGBS libraries: Use the ''High Sensitivity DNA Analysis Kits'' for 50-7,000bp. *** The sensitivity of the kit is 5pg/ul *** We can run 10 samples/chip at a time. *** Samples to be included: 24 WGBS libraries from normal control and from cancer patients. * Today I initially ran 10 samples of those libraries that were used for BSPP capture * As the library has a tight band, I need to prepare library in the range of 5-500pg to load 1ul. Richard suggested to load 1ul, I then dilute libraries to 1ng/ul in total 5ul. Note that if the size of libraries is wide, we can load as high as 10ng/ul sample. {| {{table}} border = 1 | align="center" style="width:100px;background:#f0f0f0;"|'''Sample''' | align="center" style="width:80px;background:#f0f0f0;"|'''Conc. (ng/ul)''' | align="center" style="width:80px;background:#f0f0f0;"|'''Volume to pipette (ul)''' | align="center" style="width:80px;background:#f0f0f0;"|'''H2O (ul)''' |- | NC-6||4.25||1.18||3.82 |- | NC-9||3.72||1.34||3.66 |- | NC-27||6.88||0.73||4.27 |- | NC-30||6.46||0.77||4.23 |- | 6-P-2||12.60||0.40||4.60 |- | 6-P-3||6.16||0.81||4.19 |- | 6-P-4||10.40||0.48||4.52 |- | 6-P-5||5.43||0.92||4.08 |- | cf3||9.43||0.53||4.47 |- | cf4||9.60||0.52||4.48 |}<br> * [[Media:G2938-90321_SensitivityDNA_KG_EN.pdf| '''''Instruction of Bioanalyzer High Sensitivity DNA Analysis Kits''''']] * We actually can load 11 samples. I then loaded cf4 sample in duplicates. == Result == * [[Media:2100 expert_High Sensitivity DNA Assay_DE72903057_2014-10-03_15-48-33_wgbslib.pdf| '''''Log file''''']] * From the result, it showed that there is no different of the cfDNA size between samples from normal control and cancer patients. * One thing that's weird for me is that the library size is ~300bp in 6% TBE which represent the size of cfDNA ~180. However the size of these libraries in Bioanalyzer is only ~205bp.
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