Brandon:LabNotes/Project1/2013-8-19

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New RNA processing method, No PAP, No RnIII on cells for accessibility testing


  • Had very high single read alignments (76-79% with pure DNA, and 200 ng of RNA was used for each sample. Clonal reads and unmapped reads were low. At best see 60% single read alignments for RnIII/PAP method for pure DNA, thus looking really promising.


  • Now going to test on cell samples. Recently generated IVT accessibility RNA from cell samples when testing transposition on FACS buffer and have much left over. Also can then do a direct comparison to samples processed with RNIII/PAP.


  • can also adding in Rnase H, NPA primer and polymerase into the reaction at once. However since extension will be wanted off of the NPA primer, denaturing will probably still be needed.