10x Genomics
Chromium Single Cell Immune Profiling

Cell Ranger5.0, printed on 12/04/2024

Loupe V(D)J Browser Tutorial

Welcome to the Loupe V(D)J Browser tutorial. In the next few pages, you will learn how to explore the data generated by a single Cell Ranger run on a human T cell sample spiked in with 40% CMV, 10% Flu, and 5% SARS-CoV-2 (COVID) reactive cells.

The tutorial will cover how to find and filter top clonotypes based on antigen specificity, examine V-J genes, search for CDR3 motifs, and delve deep into 10x Genomics Single Cell Immune Profiling data.

Background

This tutorial assumes some familiarity with the basic principles of both V(D)J recombination and sequencing, but here is a quick review of the terminology:

• Reads with the same cell barcode and UMI which align to the same transcript sequence are assembled into contigs.
• Each V(D)J contig contains a nucleotide sequence for one CDR3, which is identified using an evolutionarily conserved motif enclosing the V-J junction.
• Reads from contigs within the same exact subclonotype are re-assembled to create a consensus sequence.
• Each cell may have more than one chain. Cells within the same clonotype share an unmutated common ancestor during clonopoiesis. They may have a different number of chains or different CDR3 regions, but be considered part of a single clonotype.

For other terminology, refer to the Glossary.

Setup

Before beginning the tutorial, make sure to download and install Loupe V(D)J Browser. The tutorial dataset is bundled into Loupe V(D)J Browser and can be accessed by clicking on 'VDJBEAMTutorial' on the browser home page. The corresponding .cloupe is available for download.

Another way to access the tutorial dataset is by clicking on 'Load Tutorial Dataset' from the Help menu. Once the dataset is loaded, click here to explore the main user interface.

About the tutorial dataset

The sample in this tutorial dataset contains Human T cells that were spiked in with 40% CMV, 10% Flu, and 5% SARS-CoV-2 (COVID) reactive cells. The sample was labeled with CMV, Flu, EBV-BRLF1, EBV-BMLF, and COVID peptide antigens bound to the A*02:01 MHC allele. A detailed description of the dataset is provided on the public datasets page.

Next: Clonotype Distribution and Sequence