Prepare Your Runs 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 Runs metadata file, you can download one here.
  • Here are some specific instructions for filling out a Runs metadata file:
  • For the Run property, the value will look something like this: EXR-AMILO1GASTCANC-RU.
    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 run. Here, my run is related to gastric cancer, so I wrote GASTCANC.
    4. Finally, the value ends with -RU to indicate that the file is a Runs 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 - Experimental Design property, you should give a description of your experimental design.
    • Please do not leave this property blank or write "N/A" - you should write something!
  • For the - Type property, you should write "qPCR".
  • You don't need to write anything for the -- qPCR property, but don't delete it from your file!
  • Preferably, you should fill out information about your qPCR Instrument under the --- qPCR Instrument property.
    • For example, you can list information under the ---- Model property, ---- Manufacturer property, ---- Software property, etc.
  • You should keep the --* Raw Data Files property, and its value should be the total number of biosamples in your submission ("99" if you have 99 biosamples, for example).
  • Underneath the --* Raw Data Files property, you will have one --*- Biosample ID property for each biosample in your submission.
    • For example, if you have 99 biosamples in your submission, you will have 99 lines containing the --*- Biosample ID property.
    • Each line should contain a biosample ID for a different biosample (you came up with these biosample IDs earlier when filling out your Biosamples file).
  • Below each --*- Biosample ID property, you will have one --*-- DocURL property.
    • For example, if you have 99 biosamples in your submission, you will have 99 lines containing the --*-- DocURL property.
    • The value for each of these will be coll/Biosamples/doc/ and then the value of the --*- Biosample ID directly above.
  • If you have card information for your samples, you should also provide that information by filling out the --*-- Number of Cards property for each biosample.
  • You can then provide specific information about the data files associated with each biosample by filling out the --*-* Files property for each biosample with the number of files ("2", for example),
    and then listing the respective file names (under the --*-*- File Name subproperty) and card lot numbers (under the --*-*-- Card Lot Number subproperty).
    • Remember that these data files would be located in your data archive! If you don't have specific data files for each biosample, then you can skip filling out the --*-* Files property and its subproperties.
  • If you're confused by the directions above related to the --* Raw Data Files property and its subproperties, you should look at the COMPLETED RUN EXAMPLE FILE.
  • Finally, you should put the value 1 for the * Related Studies property.
    • For the *- Related Study subproperty, write the Studies ID you gave for your Studies metadata file above.
    • I would put EXR-AMILO1GASTCANC-ST.
    • For the *-- DocURL subproperty, write the same ID but in the following format: coll/Studies/doc/ and then your ID.
    • I would put coll/Studies/doc/EXR-AMILO1GASTCANC-ST.
  • 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 Run property.
    • For example, I would name my metadata file EXR-AMILO1GASTCANC-RU.metadata.tsv.
    • If you need help saving your metadata file, we have instructions available here.

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