- Data Coordination Center
- DCC Services
- Genboree Account
- What Can I Do with exRNA Profiling Data?
- RNA-seq Data
- RT-qPCR Data
- Data Repository
- Data Analysis Tools
- Metadata Standards
- Metadata Tracking UI
- Wikis, Tutorials, Discussions
- DMRR/DCC Demos at Meetings
- Contact Us - Members of the DCC
Data Coordination Center¶
The Data Coordination Center (DCC) for the Extracellular RNA Communication Consortium (ERCC) is led by Prof. Aleksandar Milosavljevic
at the Bioinformatics Research Laboratory, Baylor College of Medicine, Houston, TX, USA.
- develop data and metadata standards for the ERCC
- establish data flow into the exRNA Atlas database
- develop tools for download, visualization and analysis of exRNA data
- integrate exRNA Atlas database with other relevant resources
If you are a new user, please follow the steps below for obtaining a Genboree account and all associated services.
- Sign up for Genboree Account: You can sign up for a new Genboree account at http://www.genboree.org/. Click the Login/Register button in the top right corner and then select New Account from the dialog. Fill out the registration form with your details and hit Submit. You'll get an email asking you to confirm (typical signup/verification process).
- Log into the Genboree Commons and GenboreeKB: Next, you will need to sign in once to the Genboree Commons (used for exRNA related communications) and GenboreeKB (used for navigating exRNA metadata). You should use the username and password obtained from Step 1. Signing in once allows our system to recognize you so we can add you to the appropriate projects/sub-projects. Sign into the Genboree Commons at http://genboree.org/theCommons/login and the GenboreeKB at http://genboree.org/genboreeKB/login.
- Email Sai or William: Finally, you will need to email Sai (firstname.lastname@example.org) or William (email@example.com) to gain access to the appropriate projects/sub-projects on the Genboree Commons and GenboreeKB. We will also provide a dedicated, shared directory for your lab on our FTP server so that your lab can upload submissions for the DMRR data and metadata processing pipeline. Please include your Genboree username and PI when you email us.
What Can I Do with exRNA Profiling Data?¶
This Wiki page on FTP Data Submission Pipeline for exRNAs profiled using small RNA-seq assays outlines the different steps required to submit small RNA-seq data and metadata files through the Genboree FTP server.
This Wiki page on Data and Metadata Submission for exRNAs profiled using RT-qPCR assays outlines the different steps required to submit qPCR data and metadata files to the DCC.
exRNA Atlas is the data repository of the ERCC, which includes exRNA profiles derived from various biofluids and conditions and currently stores data profiled from small RNA sequencing assays and RT-qPCR assays.
Click here to learn more about the exRNA Atlas.
Data Analysis Tools¶
The Genboree Workbench is a web-based platform for performing data analysis using the latest bioinformatic tools. You can upload your data and perform various analyses using a "drag and drop" user interface.
Click here to get started with the Genboree Workbench.
Tutorials¶This Wiki page contains tutorials for analyzing exRNA data using the Genboree Workbench.
Detailed step-by-step instructions are provided to submit your RNA-seq samples for analysis using:
- exceRpt Small RNA-seq Pipeline for exRNA Profiling
- Long RNA-seq Pipeline Using RSEQtools
- KNIFE Circular and Linear Isoform Explorer
- DESeq2 Differential Expression Analysis Tool
- Target Interaction Finder
- Pathway Finder
This section provides an overview of the exRNA Metadata Standards developed by the Metadata and Data Standards (MADS) Working Group of the ERCC.
This tutorial shows you how to use the GenboreeKB exRNA Metadata Tracking System for submitting and managing metadata.
Wikis, Tutorials, Discussions¶
Summary of Useful Related Wikis in the Genboree Commons
This section serves as a repository of all useful Wiki pages related to data and metadata submission for the exRNA DCC.
Note that all of the links mentioned below can be found elsewhere on this page (in the "Data" and "Metadata" sections above).
- ERCC DCC Wiki
- exRNA Data Analysis Tools
- Small RNA-seq Data Submission to the DCC Using FTP
- exRNA Metadata Standards
- GenboreeKB exRNA Metadata Tracking System
DMRR/DCC Demos at Meetings¶
- May 2014 - Demo of small and long RNA-Seq pipelines at the ERCC 2nd Investigators' Meeting, May 2014, at Bethesda, MD
- November 2014 - Demo of small RNA-seq pipeline and use cases presented at the ERCC 3rd Investigators' Meeting, November 2014, at Rockville, MD
- April 2015 - Demo of small RNA-seq pipeline and use cases presented at the ERCC 4th Investigators' Meeting and ISEV Annual Meeting, April 2015, at Bethesda, MD
- May 2015 - CIBR RNA-seq workshop - Demo of exceRpt small RNA processing pipeline, May 2015, at Baylor College of Medicine, Houston, TX
- November 2015 - Data Submission & Analysis Infrastructure at the DMRR - Talk at the ERCC 5th Investigators' Meeting, November 2015, at Rockville, MD
- April 2016 - DMRR Data Analysis and Bioinformatics Workshop - ERCC 6th Investigators' Meeting, April 2016, at Bethesda, MD