Noi/NOTES/2014-10-3

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Measurement of the size distribution of WGBS libraries generated from cfDNA[edit]

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.
Sample Conc. (ng/ul) Volume to pipette (ul) 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


Result[edit]

  • 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.