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  1. IGB
  2. IGBF-2966

Investigate rice RNA-Seq paper and data

        Details

        • Type: Task
        • Status: Closed (View Workflow)
        • Priority: Major
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
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          Description

          Situation: Yiping Qi's group has identified a paper with rice protoplast single cell RNA-Seq data here. They would like us to investigate the data and see if we can use it to determine lowly expressed genes in rice sheath tissue from protoplasts.

          Task: Read through the paper and identify the data sources containing the sequence files. Also see if they have gene counts tables available.

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              Task - A task that needs to be done. IGBF-2943 Investigate recent literature on compendium databases with RNA-Seq

              • Major - Major loss of function.
              • Closed

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                nfreese Nowlan Freese added a comment -

                Here is the link to the page with the sequence data: https://ngdc.cncb.ac.cn/gsa/browse/CRA004082

                This seems to be the only location of the data, they do not appear to be in the SRA, which would explain why we didn't see them earlier.

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                nfreese Nowlan Freese added a comment - Here is the link to the page with the sequence data: https://ngdc.cncb.ac.cn/gsa/browse/CRA004082 This seems to be the only location of the data, they do not appear to be in the SRA, which would explain why we didn't see them earlier.
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                nfreese Nowlan Freese added a comment -

                Here is the link to their GitHub page with various R files used to analyze the data: https://github.com/Yuwang-art/scRNA-seq_in_rice_seedlings

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                nfreese Nowlan Freese added a comment - Here is the link to their GitHub page with various R files used to analyze the data: https://github.com/Yuwang-art/scRNA-seq_in_rice_seedlings

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                  • Assignee:
                    nfreese Nowlan Freese
                    Reporter:
                    nfreese Nowlan Freese
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