We bumped into bacterial Nudix pyrophosphohydrolase RppH which seems to do the same thing (RNA decapping). Does anyone has experience in using this enzyme for RNA processing for GRO-seq?
According to a recent patent from NEB (https://www.google.com/patents/US20120077230?dq=rpph+cap&hl=en&sa=X&ei=oFHzUbGNDsjmigLP-YH4CA&ved=0CDkQ6AEwAA) RppH should work instead of TAP, however the specific activity is about 100-fold lower, which negates the price advantage per volume. If you don't really care about sequencing the actual 5' end at base-pair resolution, you could use the A-tail/RT/circularization method published in Ingolia et al Science, 2009 for Ribo-Seq, or alternatively the 3' ligation/RT/circularization variant as described in their later paper on NET-Seq (Chruchman and Weissman, 2011, Nature). The former has been used successfully for GRO-Seq (Hah, Cell, 2011; Wang, Nature 2011), and the latter also works similarly well for RNA-Seq.
According to a recent patent from NEB (https://www.google.com/patents/US20120077230?dq=rpph+cap&hl=en&sa=X&ei=oFHzUbGNDsjmigLP-YH4CA&ved=0CDkQ6AEwAA) RppH should work instead of TAP, however the specific activity is about 100-fold lower, which negates the price advantage per volume. If you don't really care about sequencing the actual 5' end at base-pair resolution, you could use the A-tail/RT/circularization method published in Ingolia et al Science, 2009 for Ribo-Seq, or alternatively the 3' ligation/RT/circularization variant as described in their later paper on NET-Seq (Chruchman and Weissman, 2011, Nature). The former has been used successfully for GRO-Seq (Hah, Cell, 2011; Wang, Nature 2011), and the latter also works similarly well for RNA-Seq.
Are you looking for RNA decapping enzymes? Tobacco acid pyrophosphatase is out of the market right now. Here are some other alternatives for Tobacco acid pyrophosphatase . Check the following link for Tobacco Decapping Enzyme, human DCP2, and E.coli RppH