Prepare Your Submissions 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 Submissions metadata file, you can download one here.
  • Here are some specific instructions for filling out a submissions metadata file:
  • For the Submission property, the value will look something like this: EXR-AMILO1GASTCANC-SU.
    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 William.
    3. Third, I wrote GASTCANC to give some information about my submission. Here, my submission is studying gastric cancer, so I wrote GASTCANC.
    4. Finally, the value ends with -SU to indicate that the file is a Submissions 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 - Submitter property, the value will look something like this: EXR-WTHIS1-SUB.
    1. The ID will always start with EXR- (this stands for exRNA).
    2. Next, I wrote WTHIS1 because my name is William THIStlethwaite (WTHIS). The 1 indicates that I am the first submitter with this particular ID.
      If you're not sure about your submitter ID, feel free to contact William.
    3. Finally, the value ends with -SUB to indicate that the ID is a submitter ID.
    4. Make sure you also fill out the -- First Name, -- Last Name, and -- Email subproperties.
  • For the - Date property, you should write the date of your initial submission in the format: YYYY-MM-DD.
    • For example, 2017-06-05 would be valid. So would 2017-07-25.
    • Basically, you will always write the current date UNLESS you are re-using the same Submissions metadata file from a previous submission.
      In that case, you should just leave the date alone (with its original date from before).
  • For the - Last Update Date property, you should write the current date in the format: YYYY-MM-DD.
    • This is true regardless of whether you are submitting this Submissions file for the first time or re-using an old Submissions file previously submitted.
  • For the - Principal Investigator property, the value will look something like this: EXR-AMILO1-PI.
    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 William.
    3. Finally, the value ends with -PI to indicate that the ID is a PI ID.
    4. Make sure you also fill out the -- First Name, -- Last Name, and -- Email subproperties.
  • For the - Funding Source property, the value should be a description of the funding source for the current submission. Since the domain is string, you can write anything here.
    • The default value is "NIH Common Fund", and that's appropriate for any case where your submission is funded by an ERCC grant.
    • For the -- Grant Details subproperty, you should write the exact grant number associated with your submission. You can see a list of possible values in the domain column.
      You should write "Non-ERCC Funded Study" if your grant does not fall under the list of Common Fund ERCC grants.
  • We've now covered all of the required properties, but you should try to fill in the following properties as well:
    • - Organization
    • - Lab Name
    • Subproperties of - Address (you will not actually put any value for - Address itself because its domain is [valueless])
  • 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.
    • EXAMPLE 1: I didn't fill out a value for - Notes, so I'll delete it from my file.
    • EXAMPLE 2: I didn't fill out a value for - Address (because it has a domain of [valueless]), but I did fill in values for -- City and -- State.
      I will not delete - Address. However, I will delete -- Country (a subproperty of - Address) if I didn't fill in a value for it.
    • EXAMPLE 3: I didn't fill out a value for - Address, and I also didn't fill in values for any of its subproperties (-- City, -- State, etc.).
      I will delete - Address and all of its subproperties.
  • 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 Submission property.
    • For example, I would name my metadata file EXR-AMILO1GASTCANC-SU.metadata.tsv.
    • If you need help saving your metadata file, we have instructions available here.

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