Prepare Your qPCR Targets Metadata File

  • First, download the template linked here.
  • After you've opened the template, you will provide values in the value column.
  • Note that your submission will likely have multiple value columns, as you will need one value column per biosample in your submission.
    • For example, if I had 20 biosamples associated with my submission, I would create 19 additional value columns to the right of the one currently present in the template.
  • 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 qPCR Targets metadata file, you can download one here.
    • WE HIGHLY RECOMMEND YOU DOWNLOAD THE EXAMPLE, AS IT WILL MAKE UNDERSTANDING THE DIRECTIONS BELOW MUCH EASIER!
  • Here are some specific instructions for filling out a qPCR Targets metadata file:
  • For the qPCR Targets property, the value will look something like this: EXR-AMILO1GASTCANC1-QT.
    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 -QT to indicate that the file is a qPCR Targets 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 - Biosample ID property, you should write the biosample ID associated with the biosample that you'll be providing qPCR targets for.
    • For example, if I'm providing qPCR target information for the EXR-AMILO1GASTCANC1-BS biosample, I would write "EXR-AMILO1GASTCANC1-BS".
    • Remember that we came up with all our biosample IDs earlier when filling out our biosample metadata file.
    • Each value column in your qPCR Targets metadata file should have a different biosample ID.
  • For the -- DocURL property, you'll write the following: "coll/Biosamples/doc/" and then your biosample ID.
    • For example, if I wrote "EXR-AMILO1GASTCANC1-BS" for the - Biosample ID property, I would then write "coll/Biosamples/doc/EXR-AMILO1GASTCANC1-BS" for the -- DocURL property.
  • For the - Related Run ID property, you should write the ID associated with the run metadata file that you created earlier.
    • For example, if my run file had the ID EXR-AMILO1GASTCANC-RU, I would write "EXR-AMILO1GASTCANC-RU".
    • You can put this same run ID in each value column.
  • For the -- DocURL property, you'll write the following: "coll/Runs/doc/" and then your run ID.
    • For example, if I wrote "EXR-AMILO1GASTCANC-RU" for the - Related Run ID property, I would then write "coll/Runs/doc/EXR-AMILO1GASTCANC-RU" for the -- DocURL property.
  • For the * Targets property, you don't need to write anything, but don't delete it!
  • Underneath the * Targets property, you will have one *- Target Name property and one associated *-- Ct Value property for each target.
    • For example, if you have 46 targets total, you will have 46 lines containing the *- Target Name property and 46 additional lines containing the associated *-- Ct Value property.
    • Remember that each value column will contain information about this target for a particular biosample.
  • For the *- Target Name property, you should list the name of the target.
    • For the associated *-- Ct Value property, you should write the Ct value associated with that target.
    • If you want, you can also list additional information about the target, like *-- Ct Threshold, *-- Baseline Start, and *-- Baseline Stop.
  • 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 qPCR Targets property.
    • For example, I would name my metadata file EXR-AMILO1GASTCANC-QT.metadata.tsv.
    • If you need help saving your metadata file, we have instructions available here.

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