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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 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.

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:

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.