Dear Madame, dear Sir, my name is Carsten Raabe and I am writing to you because I do have difficulties in understanding certain aspects of the ENCODE RBP track annotation. The corresponding description of the RBP track states that " The tracks in this supertrack contain two forms of information: genes whose transcripts were bound by the given RBP (such as SUNY RIP GeneSt) and approximate location of the RBP binding site in the mRNA sequence (such SUNY RIP Tiling and SUNY RIP-seq)." (>>> http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=214116897&c=chr2&g=wgEncodeRbpSuper). However, if I refer to the ENCODE/SUNNY RIP-seq Method section it appears that the ilumina sequencing track contains substantially the very same information as the SUNY RIP GeneSt does . Id est " RBP-mRNA complexes were purified from cells grown according to the approved ENCODE cell culture protocols <http://genome.ucsc.edu/ENCODE/protocols/cell>. RNA samples were amplified and converted to cDNA with the Nugen <http://www.nugeninc.com> Ovation© RNA-Seq System and prepped for sequencing with the Illumina <http://www.illumina.com> mRNA-Seq protocol" and "These tracks show the associated mRNAs that co-precipitate with the targeted RNA-binding proteins using RIP-Seq profiling" (>>> http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=214116897&c=chr2&g=wgEncodeSunyRipSeq).
In conclusion I do wonder how would I get to know about the above mentioned "approximate" RNA binding site. As far as I believe to understand from here it is rather likely that we gain the same information by both methods; which would be the mRNA that is assoxaited with a RBP rather than that we understand where within the mRNA the protein would bind. Thanks a lot in advance not only for the reply but also for the server itself, which is tool that rocks. Cheers, C. _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
