10x Genomics
Chromium Single Cell Immune Profiling

Cell Ranger2.1, 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 CD8+ cytotoxic T cell sample. You'll find and explore top clonotypes and V-J genes, search for CDR3 motifs, and delve deep into sequence data to find variants and assess the validity of the consensus sequences computed by Cell Ranger's V(D)J assembly algorithms.

Background

This tutorial will mostly assume that you are familiar with the basic principles of both V(D)J recombination and sequencing, but let's review some of the terminology as we use it in the tutorial and the tools.

• 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 a motif which spans the V-J junction. This CDR3 uniquely identifies a chain.
• Reads from contigs with the same CDR3 are re-assembled to create a consensus sequence. This is an idea of what the whole chain looks like within this sample; it may be more or less similar to the reference sequence, depending on many factors.
• Each cell may have more than one chain. The set of chains in a particular cell defines its clonotype.
• Cells must have all the same chains to be part of the same clonotype, but any given CDR3 may appear in more than one clonotype.

If there are other questions about the terminology, feel free to refer to the Glossary.

We also use some of the common visual idioms and conventions you may be familiar with from other tools, such as the Integrative Genome Viewer.

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 was generated by a single-channel 10x Chromium run with nearly 2,000 CD8+ cytotoxic T cells, from the mononuclear cells of a healthy donor (AllCells catalog # PB099-3-0). More details about the tutorial dataset can be found on the public Datasets page.

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