Prepare Your qPCR Metadata Archive

'Metadata' refers to descriptive information and protocols for the overall study, the experiments performed, and the individual samples that are part of your submission.
This information is supplied by completing one file for each type of metadata and then archiving those files in your metadata archive.
Submitting your metadata is very important for:
  • ensuring a comprehensive record of your samples
  • comparing samples from various biofluids, sample collection protocols and analytical protocols
  • replication of experiments
    and so on.
Your metadata archive will contain seven different files, with one optional file:
  • Submissions metadata file
  • Studies metadata file
  • Experiments metadata file
  • Donors metadata file
  • Biosamples metadata file
  • Runs metadata file
  • qPCR Targets metadata file

We will go step-by-step below to create these files.

Step 1. Open Your Reference Materials (Introduction)

  • The basic workflow for creating each metadata file is:
    • Download appropriate template (linked below in each section)
    • Fill in values
    • Delete rows that contain unused properties
    • Remove any empty rows (and stick together all remaining rows)
    • Save metadata file
  • Each template is a tab-delimited file that can be opened in a standard text file viewer (like Notepad++ or BBEdit).
  • Each template can also be opened in a spreadsheet application like Microsoft Excel. More instructions on using Excel to view a given template can be found here.
  • In order to check values enforced by ontologies, you will need to access a particular project on the GenboreeKB website.
    • To check whether you have permission to access this project, click here.
    • If you receive an error message informing you that the "Current Redmine user is not a member of the private Redmine project containing this GenboreeKB", then contact the exRNA Team to fix this issue.

Step 2. Prepare Your Submissions Metadata File

  • IMPORTANT: If you've completed a submission in the past, it's possible that you can re-use the same Submissions metadata file for your current submission.
    If the metadata is exactly the same for both submissions (same PI, same submitter, same grant number, etc.), then you can re-use the old Submissions metadata file
    and skip the instructions below. All you will need to do is update the - Last Update Date property with the current date.

Step 3. Prepare Your Studies Metadata File

  • IMPORTANT: If you've completed a submission in the past, it's possible that you can re-use the same Studies metadata file for your current submission.
    If you're merely submitting a new Run underneath the same Study (same study title, same authors, same anticipated data repository, etc.),
    then you can re-use the old Studies metadata file and skip the instructions below.

Step 4. Prepare Your Experiments Metadata File

Step 5. Prepare Your Donors Metadata File

Step 6. Prepare Your Biosamples Metadata File

Step 7. Prepare Your qPCR Runs Metadata File

Step 8. Prepare Your qPCR Targets Metadata File

Step 9. Move All Metadata Files to Same Directory

  • After you've created your seven metadata files, you'll want to make sure that they're all in the same directory.
    • This directory should only contain these seven files - no extra folders, no other files, etc.

Step 10. Validate the Metadata Files

  • You can validate the generated metadata files by going to https://exrna-atlas.org/exat/submission/validation or it can also be found under "More" -> "Metadata Submission Validator" in the exRNA Atlas page https://exrna-atlas.org
    • Select the metadata entity type (Biosample, Donor, Analysis, etc.) in the drop down.
    • Select the metadata file (Must be in multi-column tabbed TSV format)
    • Click on Validate
  • *Note: Runs Metadata file may return an Invalid for "Run.Type.small RNA-seq" where "Raw Data Files" are missing. This field will be filled by the pipeline and you can proceed to submit the Runs metadata if this is the only error.

Step 11. Create Metadata Archive

  • Place all metadata files into a single archive.
    • The archive must be .tar.gz or .zip format.
  • The metadata archive's file name must end in _qPCR_metadata.
    • For example, "samples_qPCR_metadata.zip" would be valid. So would "exRNA_qPCR_metadata.tar.gz".
  • The prefix for the file name must match the data archive's file name.
    • For example, if my data archive is named "samples_qPCR_data.zip", then my metadata archive should be named "samples_qPCR_metadata.zip".
  • If you need help creating an archive, please visit the Creating an Archive page.

Summary

  1. Open your reference materials
  2. Complete each metadata file type in turn (a total of seven different metadata file types)
  3. Move all completed metadata files to the same directory
  4. Compress all metadata files into one archive (with qPCR_metadata suffix and with same prefix as the data archive you created earlier)

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