RNA integrity and quality control of XRNAX extracts
XRNAX user feedback has identified problems with RNA stability during DNase digestion, which could be traced back to the use of TURBO DNase (Ambion, AM2238). Please note that for the best XRNAX results, we recommend NEB DNase I (RNase-free) (NEB, M0303L) in combination with its recommended buffer and the RNase inhibitor RNasin Plus (Promega, N2511).
RNA degradation in an XRNAX sample can be identified by following the quality control (QC) steps, which are described in 'the protocol' section of this website. Indicators of RNA degradation include low yield of RNA in an XRNAX extract, as assessed through UV spectroscopy. While yields vary depending on the cell line, a typical XRNAX experiment from 40 million MCF7 cells, crosslinked at 254 nm, 200 mJ/cm^2, should yield between 200-400 µg RNA. Yields for HeLa and HEK293 cells are usually higher.