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  1. IGB
  2. IGBF-3923

Add cool new Arabidopsis dataset to RNA-Seq Quickload

        Details

        • Type: Task
        • Status: To-Do (View Workflow)
        • Priority: Major
        • Resolution: Unresolved
        • Affects Version/s: None
        • Fix Version/s: None
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          Description

          There is a cool new short-read RNA-Seq data set from an exciting new paper that investigates splicing biochemistry in Arabidopsis. Not a lot is known about the biochemistry of splicing in plants, and this article is a breakthrough, in my opinion!

          Here is the link to the article:

          https://rdcu.be/dVeKn

          Here is the link to the dataset:

          https://www.ebi.ac.uk/ena/browser/view/PRJEB65251

          This dataset would be a good way to show off IGB's usefulness for studying splicing regulation in plants. We could use this to showcase not just the software, but also a cool new discovery in plant biology.

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              ann.loraine Ann Loraine added a comment - - edited

              I haven't put this into a sprint. I'd love to get comments from Nowlan Freese, Paige Kulzer and Robert Reid regarding feasibility, value of doing this, etc. What do you think?

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              ann.loraine Ann Loraine added a comment - - edited I haven't put this into a sprint. I'd love to get comments from Nowlan Freese , Paige Kulzer and Robert Reid regarding feasibility, value of doing this, etc. What do you think?
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              robofjoy Robert Reid added a comment -

              Should we journal club this paper? Could do it as a Wednesday Noons session, inviting other Ktown people. Or we could do it as a smaller group also.
              R

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              robofjoy Robert Reid added a comment - Should we journal club this paper? Could do it as a Wednesday Noons session, inviting other Ktown people. Or we could do it as a smaller group also. R
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              pkulzer Paige Kulzer added a comment -

              I think it would be nice to have a dataset in IGB that could be used to demonstrate splicing, especially for someone like me who hasn't had much experience with plant data and still doesn't completely understand what IGB's capabilities are in terms of visualizing splicing regulation. Plus, from a data point of view, all of the samples are in BAM format which would make for a relatively easy Quickload creation!

              Show
              pkulzer Paige Kulzer added a comment - I think it would be nice to have a dataset in IGB that could be used to demonstrate splicing, especially for someone like me who hasn't had much experience with plant data and still doesn't completely understand what IGB's capabilities are in terms of visualizing splicing regulation. Plus, from a data point of view, all of the samples are in BAM format which would make for a relatively easy Quickload creation!

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                • Assignee:
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                  Reporter:
                  ann.loraine Ann Loraine
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                    Updated: