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.
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