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Cell Ranger


10x Genomics
Chromium Single Cell Immune Profiling

What is Cell Ranger for Immune Profiling?

Table of Contents


Adaptive immunity is based on clonal selection and expansion from a repertoire of T and B lymphocytes bearing a diversity of cell-surface receptors and antibodies that recognize specific antigens. The enormous diversity of lymphocyte receptors and antibodies expressed from a relatively small number of gene segments is largely made possible through V(D)J recombination. The hypervariable recombined V(D)J transcripts in turn determine the affinity of the Complementary Determining Regions (CDRs) to bind to specific epitopes. See the Glossary for more details.

The 10x Genomics 5' Chromium Next GEM Single Cell Immune Profiling Solution enables simultaneous analysis of these libraries at single cell resolution for the same set of cells:

This makes the Immune Profiling Solution ideal for understanding the key features of an adaptive immune response and their impact on other genomic analytes, disease severity, therapy, and outcome.

Paired TCR and BCR sequences

Paired T or B cell receptor sequences are obtained per cell by partitioning thousands of cells into nanoliter-scale Gel Beads-in-Emulsion (GEMs). All cDNA generated in a single GEM share a common 10x Barcode. Inside a GEM, one to several UMIs are captured for each V(D)J chain. A round of enrichment PCR targeting the 5′ end to the C-region, followed by enzymatic fragmentation results in a pool of molecules originating from the same transcript. The molecules carry the same 10x Barcode and UMI sequences, but with different insert lengths, resulting in different sequence start points. The diversity of start points gives complete coverage of the targeted portion of each V(D)J transcript, which is typically ~650 bp.

Data analysis with Cell Ranger

Analysis of these data types can be performed using the latest versions of Cell Ranger. The following illustration depicts how the cellranger multi pipeline can be used to analyze FASTQ data derived from these three Immune Profiling library types from the same GEM Well:

Ways to run Cell Ranger

  1. Run Cell Ranger on 10x Genomics Cloud Analysis

Skip Cell Ranger download and installation and get started with 10x Genomics Cloud Analysis, our recommended method for running Cell Ranger pipelines for most new customers. Use your web browser to easily generate Cell Ranger outputs from your FASTQ files and aggregate outputs from multiple runs, free for every 10x Genomics sample. Currently available only in the United States and Canada. Sign up for a free account or view tutorials and learn more.

  1. Install and run Cell Ranger on your own computing infrastructure

Learn how to install and run Cell Ranger.

Cell Ranger pipelines

Cell Ranger includes five pipelines relevant to Immune Profiling data analysis:

The .cloupe files and the .vloupe files output by the pipelines can be overlaid for an integrated analysis with Loupe Browser and Loupe V(D)J Browser. Refer to Analysis of Multiple Library Types for more information.

Supported libraries

The libraries supported by different versions of Cell Ranger:

Single Cell Immune Profiling Solution CR 7.1 CR 7.0 CR 6.1 CR 6.0 CR 5.0 CR 4.0 CR 3.1 CR 3.0 CR 2.2
5’ Gene Expression
V(D) J
5’ Gene Expression + V(D) J
5’ Gene Expression + Cell Surface Protein
5’ Gene Expression + Cell Surface Protein + V(D) J
V(D) J Enriched + Cell Surface Protein
5’ Cell Surface Protein only
Targeted Gene Expression
5’ HT (High Throughput)
5’ Gene Expression + CRISPR
5’ Gene Expression + CRISPR + Cell Surface Protein
5’ Gene Expression + CRISPR + V(D)J Enriched Libraries
5’ Gene Expression + Antigen Capture + V(D)J ± Cell Surface Protein