Hello, Miler,
This does sound like an interesting dataset. We would like to
provide it to our users. The timeframe for release depends to
some extent on how much of the data formatting you do yourselves.
Have you made custom tracks of the data for our own use already?
Please reply directly to me offlist and we will see what can
be done.
regards,
--b0b kuhn
ucsc genome bioinformatics group
On 2/22/2012 7:20 AM, Miler Lee wrote:
> Hello,
>
> We're potentially interested in providing some tracks to include in
> the public Zebrafish Genome Browser. Our lab (headed by Antonio
> Giraldez, Yale University Dept. of Genetics) has generated a set of
> ribosome profiling experiments for early Zebrafish embryos, which we
> feel may be of great benefit to the Zebrafish research community.
> Ribosome profiling quantifies mRNAs bound by ribosomes, using high
> throughput sequencing, and thus is a measure for translational
> activity; this method was pioneered by Ingolia et al, 2009 (Science,
> DOI: 10.1126/science.1168978). We envision providing Wiggle tracks
> similar to the U Mass CHiP-Seq data that show ribosome occupancy
> levels, as well as tracks that show input RNA seq signal, over 3 timepoints.
>
> We'd appreciate it if you could provide us information about how to
> begin this process, any sort of guidelines that you would need us to
> follow, and the timeline for submission and subsequent release of the
> data that is typical. These data are in support of a publication that
> is currently under re-review, so we anticipate wanting to make these
> data public as soon as possible after acceptance.
>
> thanks much,
> Miler Lee
>
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