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 "small RNA-Seq".
  • You don't need to write anything for the -- small RNA-Seq property, but don't delete it from your file!
  • For the --- Sequencing Instrument property, your value will be enforced by ontologies.
    • The following are commonly used values for this property:
      • Illumina HiSeq 2000, Illumina Genome Analyzer IIx, Illumina MiSeq
    • If your sequencing instrument is not listed above, then follow these steps:
      1. Visit the GenboreeKB UI template for Runs (you will need to log into your GenboreeKB account if not already logged in) here.
      2. Double click the pencil icon next to the Sequencing Instrument property.
      3. Begin typing the name of your sequencing instrument. After you type at least 3 characters, our look-ahead search will attempt to find matching terms in the ontology.
      4. Any term that pops up will be a valid value for your property. You can copy paste it into your Runs metadata file.
    • If you still can't find an appropriate term for your sequencing instrument, feel free to contact William.
  • You don't need to write anything for the ---Experiment Details property, but don't delete it from your file!
  • Fill in a value for the ----Directionality property. You can either put Strand-specific or Non-strand-specific.
  • Fill in a value for the ----Run Type property. You can either put Single-end or Paired-end.
  • Fill in a value for the ----Maximum Read Length property. You should put an integer followed by nt (the units).
    • For example, "50 nt" would be a valid value.
  • 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.

Also available in: HTML TXT