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Overview of RNA preparation for CAP-MAP analysis. Cellular RNA is purified on oligo dT-conjugated beads and digested with P1 nuclease to release cap dinucleotides and nucleotide monophosphates. The synthetic cap standard, ARCA, is added to the digested nucleotides. The sample is run on a PGC column coupled to a triple quadrupole mass spectrometer operating in negative ion mode and programmed to detect cap dinucleotides in the MRM mode.
