How to Download Data from ImmPort

Looking for the AMP RA Phase I data (SDY998)? You're in the right place.

ImmPort is the official repository for this dataset, but downloading files requires a few setup steps. This guide walks you through the entire process—from creating an account to loading data in R.

Step 1: Find the study on ImmPort

Start by visiting the ImmPort study page for SDY998:

Open SDY998 on ImmPort →

You can also find this link on the AMP RA Phase I page or the GitHub repository.

Screenshot showing the ImmPort link on the immunogenomics website — The ImmPort link is listed in the "Download Data" section.

Step 2: Create an ImmPort account

To download files, you’ll need a free ImmPort account. Click Study Package (Web) in the top navigation under “Download Options”.

Screenshot showing the Register button on ImmPort — Click "Register" to create a new account.

Since downloads require registration, you will be redirected to a login and registration page. Now click Register and fill out the registration form with your details.

Screenshot of the ImmPort registration form — Complete the registration form. You'll receive a confirmation email.

Tip: Use your institutional email address if you have one—it may speed up account approval.

Step 3: Log in to ImmPort

Once your account is confirmed, log in using your credentials.

Screenshot of the ImmPort login page — Enter your email and password to log in.

Step 4: Install Aspera Connect

ImmPort uses IBM Aspera Connect for fast, reliable file transfers. You’ll need to install both the browser extension and desktop application.

Screenshot of the Aspera Connect installation prompt — Follow the prompts to install Aspera Connect.

Why Aspera? Standard HTTP downloads would take hours for large genomics files. Aspera uses a faster transfer protocol that can be 10-100x quicker.

Step 5: Download and read the README

Before downloading data files, take a moment to understand what’s available. Navigate to:

Browse Shared Data → SDY998 → ResultFiles → RNA_sequencing_result

Screenshot showing navigation to ResultFiles — Navigate through the folder structure to find the RNA sequencing results.

Screenshot showing the RNA_sequencing_result folder — The RNA_sequencing_result folder contains processed data files.

Download the README file first—it describes each file and helps you identify exactly what you need.

Screenshot showing the README file — The README explains the contents and format of each data file.

Step 6: Download the data files

Select the files you need for your analysis and click to download. Aspera Connect will handle the transfer.

Screenshot showing file download interface — Click on files to download them via Aspera Connect.

Common files you might need:

Gene expression matrices (counts or TPM)
Cell metadata and cluster annotations
Sample metadata

Step 7: Load the data in R

Once downloaded, you can load the data files in R for analysis.

Screenshot showing R code to load data — Example R code for reading the downloaded data files.

For detailed analysis examples, check out the amp_phase1_ra GitHub repository.

You're all set!

You now have access to the AMP RA Phase I single-cell RNA-seq data. If you use this data in your research, please cite:

Zhang F, Wei K, Slowikowski K, et al. Defining Inflammatory Cell States in Rheumatoid Arthritis Joint Synovial Tissues by Integrating Single-cell Transcriptomics and Mass Cytometry. Nature Immunology (2019). doi:10.1038/s41590-019-0378-1

Still need help?

If you run into any issues following this guide, feel free to reach out. We're happy to help.