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10x Genomics
Chromium Single Cell Immune Profiling

What is Cell Ranger for Immune Profiling?

Single Cell V(D)J + 5′ Gene Expression + Feature Barcode Technology

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 Chromium Single Cell Immune Profiling Solution enables simultaneous analysis of the following:

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.

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

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

The .cloupe files output by cellranger count and the .vloupe files output by cellranger vdj 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.