Hello Adnan, Thanks for offering the data. Assuming that it comes with no restrictions, we are happy to host it. I will be in touch with you off-list for the logistics.
Regards, ---------- Ann Zweig UCSC Genome Bioinformatics Group http://genome.ucsc.edu On 1/4/11 7:31 PM, Derti, Adnan wrote: > Hello. > > My colleagues and I have developed a high-throughput sequencing method > that identifies polyadenylation sites in a quantitative and > strand-specific manner. We're about to submit a manuscript that > describes the method as well as a sizeable data set that we've generated > on an Illumina sequencer. We're making the data public now (i.e., > depositing reads and alignments in GEO and SRA), and we'd like to know > if UCSC would be interested in making our alignment tracks public. > > The data consists of a mixture of 22 tissues in human, mouse, rat, dog > and rhesus; they're mostly normal tissues, but the human samples include > brain and UHR MAQC samples, as well as a breast tumor and matched > normal. In each tissue, we sequenced several tens of millions of 76-bp > reads (details will follow pending interest). > > An example is attached that shows wiggle tracks for a human gene; for > simplicity, only reads for the sense strand are shown. The first figure > is on a linear scale and shows that a single polyadenylation site > dominates across all tissues. The second figure is a close-up of the 3' > UTR on a log scale; it shows that multiple polyadenylation variants are > present in every tissue, and that the UCSC and Refseq transcripts > correspond to minor polyadenylation sites. > > We developed a computational method to filter false positives arising > from internal poly-A tracts. We would suggest a super-track for each > tissue that shows four tracks, namely reads from the forward and reverse > strands in separate colors, and all reads vs. filtered reads in distinct > shades. > > <<human.agpat6.polyA.png>> <<human.agpat6.polyA.zoom.log.png>> > > Thanks, and please let me know if you'd like me to provide additional > information. > > Adnan Derti > Senior Research Scientist > Merck Research Laboratories > Boston, MA > Notice: This e-mail message, together with any attachments, contains > information of Merck& Co., Inc. (One Merck Drive, Whitehouse Station, > New Jersey, USA 08889), and/or its affiliates Direct contact information > for affiliates is available at > http://www.merck.com/contact/contacts.html) that may be confidential, > proprietary copyrighted and/or legally privileged. It is intended solely > for the use of the individual or entity named on this message. If you are > not the intended recipient, and have received this message in error, > please notify us immediately by reply e-mail and then delete it from > your system. > > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
