Analysis of Transcriptional Profiling of Immune Cells at the Single-Cell Level

  • Annabel Ferguson
  • Kong ChenEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 2111)


RNA sequencing has proven to be a key innovation for the study of biological processes by enabling scientists to measure differences in gene expression in different tissues.With recent advances in sequencing technology, researchers are able to measure gene transcription at the single-cell level, revealing previously unknown diversity and specificity of immune cells. The single-cell sequencing method now enables profiling of the T-cell receptor (TCR) genes resulting from V(D)J recombination.Here we describe how to adapt single-cell RNA sequencing data generated using the 10× genomics 5′V(D)J immune cell profiling workflow for integration into the R analysis pipeline.We will start with the data matrix files generated from the 10× genomics Cell Ranger alignment software and detail how to format this data as input for the R analysis package called Seurat such that data from both the overall cell transcript abundance and the targeted V(D)J transcript abundance data can be visualized on the same plots.

Key words

10× genomics V(D)J Drop-seq Single-cell RNA sequencing T-cell receptor repertoire profiling 



This work was supported by NIH grant R01HL137709.


  1. 1.
    Lythe G, Callard R, Hoare RL, Molina-Paris C (2016) How many TCR clonotypes does a body maintain? J TheorBiol 389:214–224Google Scholar
  2. 2.
    Murphy K, Weaver C (eds) (2017) Janeway’simmunobiology, 9th edn. Garland Science, Taylor & Francis Group, New York, p 499Google Scholar
  3. 3.
    R toolkit Seurat. Accessed 22 Mar 2019
  4. 4.
    Butler A, Hoffman P, Smibert P, Papalexi E, Satija R (2018) Integrating single-cell transcriptomic data across different conditions, technologies, and species. Nat Biotechnol 36:411–420CrossRefGoogle Scholar
  5. 5.
    10x Genomics Support. Accessed 22 Mar 2019
  6. 6.
  7. 7.

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2020

Authors and Affiliations

  1. 1.Division of Pulmonary, Allergy, and Critical Care Medicine, Department of MedicineUniversity of PittsburghPittsburghUSA

Personalised recommendations