Prepare Your longRNAseq Studies Metadata File

  • First, download the template linked here.
  • After you've opened the template, you will provide values in the value column.
  • At this point, if you haven't created a metadata file before, you should read through the Understanding the Nested Tabbed Format page to better understand how your file is formatted.
  • You are only required to provide values for those properties which have TRUE in the required column.
    • Even if a property has TRUE in the required column, if its parent property does NOT have TRUE in the required column, then you are not required to fill in the (sub) property.
  • If you want to see a completed Studies metadata file, you can download one here.
  • Here are some specific instructions for filling out a Studies metadata file:
  • For the Study property, the value will look something like this: EXR-AMILO1GASTCANC-ST.
    1. The ID will always start with EXR- (this stands for exRNA).
    2. Next, I wrote AMILO1 because my PI is Aleksandar MILOsavljevic (AMILO). The 1 indicates that he is the first PI with this particular ID. If you're not sure about your PI ID, feel free to contact the exRNA Team .
    3. Third, I wrote GASTCANC to give some information about my study. Here, my study is studying gastric cancer, so I wrote GASTCANC.
    4. Finally, the value ends with -ST to indicate that the file is a Studies file.
  • For the - Status property, you can write either "Add" or "Protect".
    • Write "Add" if you want to add your files to the public Atlas immediately.
    • Write "Protect" if you want to keep your files in the consortium-only Atlas until the embargo period ends on your submission.
  • For the - Title property, you should write an appropriate title for your study.
    • The title has to be unique when compared to every other study file in our database, so write something specific for your particular study,
      and don't re-use an old title from a previous submission!
  • For the - Type property, you should write "Long RNA-seq".
  • For the - Abstract property, you should fill in an abstract for your study.
    • Please do not leave this property blank or write "N/A" - you should write something!
    • If there's no associated publication for your study (and you haven't yet prepared an abstract), then just write a brief description of the study.
  • For the * Authors property, you should write the total number of authors associated with your study (1, 5, 10, etc.).
    • Note that this property is an item list. Thus, below the * Authors property, you will have a
      *- Author Name row and a *-- Role row (in that order) for each author associated with the study.
      You will need to add additional *- Author Name and *-- Role rows to the template if your study has more than one author.
    • For each *- Author Name row, write an author name.
    • For each *-- Role row, you will write PI, Co-PI, Submitter, or Member.
      • Write PI if the author is the main PI on the study.
      • Write Co-PI if the author is a co-PI on the study.
      • Write Submitter if the author is the person who is submitting the study to the Atlas.
      • Write Member if the author is anyone else (but is still an author).
  • For the - Anticipated Data Repository property, you should write an anticipated data repository for your study (if known).
    • You can see the different possible values for this property in the domain column for the row.
    • If you write "Other", then please also fill out a value for the -- Other Data Repository property.
    • If you write "dbGaP" or "Both GEO & dbGaP", then please also fill out a value for the -- Project registered by PI with dbGaP? property
      and the --- All data and metadata submitted to dbGaP? property.
  • If your study is associated with any publications that have PubMed IDs, then write the number of publications for the * References property,
    and then put one *- PubMed ID row for each associated PubMed ID.
  • If your study is associated with any publications that don't have PubMed IDs, then write the number of publications for the * Other References property,
    and then put one *- Reference row for each associated reference.
  • Finally, you should put the value 1 for the * Related Submissions property.
    • For the *- Related Submission subproperty, write the Submissions ID you gave for your Submissions metadata file above.
    • I would put EXR-AMILO1GASTCANC-SU.
    • For the *-- DocURL subproperty, write the same ID but in the following format: coll/Submissions/doc/ and then your ID.
    • I would put coll/Submissions/doc/EXR-AMILO1GASTCANC-SU.
  • If you didn't fill out a value for a property, then please delete the row containing that property from your file. Make sure that you actually remove the row entirely and don't leave a blank row!
    However, if the domain for the property is [valueless] and you filled out values for any subproperties, then don't delete the row.
  • Finally, save your metadata file in tab-delimited format with a file name that ends in .metadata.tsv.
    • I recommend you name your metadata file after the value given for your Study property.
    • For example, I would name my metadata file EXR-AMILO1GASTCANC-ST.metadata.tsv.
    • If you need help saving your metadata file, we have instructions available here.

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