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New study for Neurofibromatosis Type 1 Plexiform Neurofibroma Derived Tumor Lines (Edu Serra lab) #1973

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anngvu opened this issue Dec 11, 2023 · 0 comments · May be fixed by #1974
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4 of 9 tasks

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@anngvu
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anngvu commented Dec 11, 2023

Please keep this checklist for curation of a new study.

  • create an issue on datahub before curating a study (one issue per study) and copy this checklist to the issue tracker
  • List information of the dataset/paper in the issue, e.g. pmid, paper link, suppl file link
    Description: Small set of expression data to compare plexiforme neurofibroma cell lines.
    Paper: Carrió M et al. Reprogramming Captures the Genetic and Tumorigenic Properties of Neurofibromatosis Type 1 Plexiform Neurofibromas. Stem Cell Reports. doi: 10.1016/j.stemcr.2019.01.001
  • Document the curation process, e.g. how and by whom the data was transformed
    The The Neurofibromatosis Therapeutic Acceleration Program org funded NF-OSI team at Sage to process the data and submit to the public cBioPortal for a selection of their funded studies. Processing pipelines are described here: NPD-Nextflow Data Processing & Configuration-161122-155435.pdf.
  • Follow the data checklist
  • Create a pull request to datahub once the data is curated
  • Push to triage portal
  • Import into msk and public portal database
  • Update the default quick select study list see options for selecting tcga + non-tcga studies cbioportal#5831 (only for studies that are not overlapping with existing ones; only for human tumors, not cell lines)
  • Update cBioPortal news
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