10x Genomics
Chromium Single Cell Immune Profiling

Cell Ranger4.0, printed on 11/05/2024

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 peripheral blood mononuclear T cell (PBMC) sample. The tutorial will cover how to find top clonotypes and V-J genes, search for CDR3 motifs, and delve deep into 10x Genomics Single Cell Immune Profiling data.

Background

This tutorial will mostly assume familiarity with the basic principles of both V(D)J recombination and sequencing, but let's review some 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 you have downloaded and installed Loupe V(D)J Browser. If this is your first time working with Loupe V(D)J Browser, you can access the tutorial dataset by clicking on the first dataset on the Recent Files page:

You can also access the tutorial dataset by clicking on 'Load Tutorial Dataset' from the Help menu. Once you've loaded the dataset, click here to explore the main user interface.

About the Tutorial Dataset

The sample in the tutorial contains PBMCs from a healthy donor. More details about the tutorial dataset can be found on the public Datasets page.

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