Prepare Your Experiments 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 may have multiple experiments associated with it.
  • It's easy to handle multiple experiments - just create a new value column for each additional experiment.
  • For example, if I had 3 experiments associated with my submission, I would create two 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.
  • In particular, since you may be working with multiple value columns, make sure that you read through the One Nuance of Multiple Value Columns section.
• 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.

• There are many different properties present in the Experiments metadata file, but very few are required. You should just fill in all of the information you can!

• If you want to see a completed Experiments metadata file, you can download one here.

Here are some specific instructions for filling out an Experiments metadata file:

• For the Experiment property, each value will look something like this: EXR-AMILO1GASTCANC1-EX.
  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 GASTCANC1 to give some information about my experiment. Here, my experiment is related to gastric cancer, so I wrote GASTCANC and then 1 (because we're discussing the first value currently).
  4. Finally, the value ends with -EX to indicate that the file is an Experiments file.
  • If I had a second experiment, I would write something like EXR-AMILO1GASTCANC2-EX in my second value column.

• 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.

• If you want to provide information about your exRNA source isolation protocol, then leave the - exRNA Source Isolation Protocol property in your metadata file.
  • You should then, at a minimum, provide values for the following properties:
    • -- Protocol Description - provide a description of the protocol.
    • -- Biofluid - leave the value(s) for this property blank (but it is required to be in your metadata file).
    • --- Cell Removal Step Done - indicate whether cell removal step was performed (write Yes or No).
  • Preferably, you should also give more information by filling out properties like -- Cell Culture Supernatant and its subproperties (if relevant), ---- Cell Removal Method and its subproperties, etc.

• If you want to provide information about your extracellular vesicle isolation protocol, then leave the - Extracellular Vesicle Isolation Protocol property in your metadata file.
  • You should then, at a minimum, provide values for the following properties:
    • -- Protocol Description - provide a description of the protocol.
  • Preferably, you should also give more information by filling out properties like -- Density Gradient Centrifugation, -- Gel Filtration, etc.

• If you want to provide information about your exRNA sample preparation protocol, then leave the - exRNA Sample Preparation Protocol property in your metadata file.
  • You should then, at a minimum, provide values for the following properties:
    • -- Protocol Description - provide a description of the protocol.
    • -- Pre-purification of Extracellular Vesicles - indicate whether any steps were taken to pre-purify extracellular vesicles (write Yes or No).
    • -- exRNA Quantification Method - indicate method used for exRNA quantification (possible values include Ribogreen, Bioanalyzer, Nanodrop, and Other).
      • If you choose Other, you should also fill in a value for --- Other exRNA Quantification Method.

• For the - Experiment Type property, you should write longRNA-Seq.
  • Ideally, you should then keep the -- longRNA-Seq property and fill out --- Library Generation (and subproperties),
    --- Amplified (and subproperties), etc.

• 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 Experiment property (excluding the identifying number at the end if you have multiple documents).
  • For example, I would name my metadata file EXR-AMILO1GASTCANC-EX.metadata.tsv.
  • If you need help saving your metadata file, we have instructions available here.