RT-qPCR Data Submission to DCC

Quantitative PCR with reverse transcription is one of the commonly used assay in addition to RNA-sequencing to characterize extracellular RNAs.
This Wiki page includes instructions on how to submit your RT-qPCR data with accompanying metadata to the Data Coordination Center (DCC).

This tutorial will walk you through the entire process of creating an FTP account, formatting and submitting your data and metadata properly,
and then viewing your data in the exRNA Atlas. All submitted samples will be manually curated by the DCC Staff. This is a temporary curation/validation step,
until the FTP Data/Metadata Submission pipeline for qPCR data is made available.

Step 0: Getting an FTP Account on the Genboree FTP Server

Creating Your FTP Account

Files Needed for Data Submission

Your submission will consist of two different files:
  • a data archive: - The data archive will contain all of your different data files (RDML format or any other custom format provided by the qPCR instrument).
  • a metadata archive: - The metadata archive will contain various metadata documents relating to your data submission.

IMPORTANT NOTE
Both files must have the same basic file name, other than the data archive file name ending in _data and the metadata archive file name ending in _metadata.
This will be explained in more detail below, but your files will look something like this:

  • qPCR_samples_data.zip
  • qPCR_samples_metadata.zip

Here, I've chosen the name "qPCR_samples" for my submission. This is just an example - you should give a more descriptive name in your actual submission ("alzheimersDiseaseMay2016-UH2_data.zip", for example).

Step 1: Preparing Your Data Archive

Prepare Your qPCR Data Archive

Step 2: Preparing Your Metadata Archive

Prepare Your Metadata Archive
You can follow the instructions given in the above link to prepare your metadata documents. Ensure that your metadata contains information relevant to the qPCR assay i.e. all relevant qPCR metadata fields in each collection should be filled out.

Download Metadata Models, Document Templates and Example Metadata Documents

This section provides templates for each document type that will allow you to easily and quickly fill out your TSV files using Microsoft Excel or any simple word processor.
LAST UPDATED: June 22nd, 2016

  • If you are interested in building a metadata document, first download the appropriate template ("Biosamples Doc Template" template if you're building a "Biosample" document, for example).
  • You can click the link in the column named Template in GenboreeKB UI and use it for preparing your metadata document or checking the correct ontology terms for your metadata property.
    • The KB used for these templates is a "testing ground" and will not be used for any final submission of metadata. Feel free to experiment, save your completed template as a document, etc.
    • Once you've saved your document, you can download it and use it in your FTP submission (where it will be submitted to the Atlas).
    • The Metadata Submission Using GenboreeKB UI page will provide more information on navigating the GenboreeKB UI.
      IMPORTANT NOTE: You should be logged in with your Genboree user name and password to use the KB UI.
Schema Description Doc Template For Editing in Excel User Submitted qPCR Metadata Examples Template in GenboreeKB UI
Submissions TABBED Model Information about PI / submitter associated with submission. Submission Template EXR-JSAUG1UH2001-SU Submission KB Template
Studies TABBED Model A study groups together experiments or analyses for public data release purposes. Study Template EXR-JSAUG1UH2001-ST Study KB Template
Runs TABBED Model A run contains sequencing reads submitted in data files. Run Template EXR-JSAUG1UH2001-RU qPCR Run KB Template
Experiments TABBED Model An experiment contains instrument and library preparation information and groups together one or more runs. Experiment Template EXR-JSAUG1UH2001-EX qPCR Assay KB Template
Donors TABBED Model Information about each individual donor who contributed biosamples. Donor Template Donor Multi-tabbed Donor KB Template
Biosamples TABBED Model Detailed information about the sequenced sample, biofluid source, etc. Samples can be used in any number of experiments. Biosample Template ; Multi-tabbed Format Biosamples Multi-tabbed Format Biosample Biofluid KB Template Biosample Cell Culture Supernatant KB Template
Analyses TABBED Model An analysis contains secondary analysis results. Analysis Template EXR-JSAUG1UH2001-AN qPCR Analysis KB Template
qPCR Targets TABBED Model The qPCR Targets document contains the list of all targets and the corresponding Cq values for each biosample. qPCR Targets Template qPCR Targets Multi-tabbed qPCR Targets KB Template

Step 3: Uploading Your Submission to the FTP Server for Validation

Upload Submission to the DCC

Step 4: Viewing Your Results

Viewing Your qPCR Data in the exRNA Atlas

Miscellaneous Tips and Tricks

Below, you'll find some useful tips and tricks for creating your submission.

Creating an Archive

Creating an Archive

Learning How to Use the Terminal

If you need help navigating the terminal (and want to learn some basic Linux/OSX commands), the following links will be useful:

Also available in: HTML TXT