microbiome block

5’ Single cell RNA sequencing-10XGenomics MRL


Chromium Single Cell Immune Profiling allows analysis of full-length, paired B-cell or T-cell receptor (BCR/TCR) sequences, surface protein expression, antigen specificity, and 5’ gene expression, all from a single cell. Scale up with a high-throughput solution, or focus on key genes with targeted gene expression panels. This assay uses a Gel Bead-in-Emulsion (GEMs) concept to capture individual cell signals. In this workflow, three libraries are constructed that include a 5’ gene expression library, one TCR library and one BCR library. About 10K individual cells are input in each library and 30-40K paired sequencing reads are generated on gene expression library and 5-10k reads on TCR and BCR library. These libraries are sequenced on NovaSeq6k platforms to generate 300-500 Million sequences per sample. RAW sequencing data is analyzed using Cell Ranger pipeline and visualized through Loupe browser tools.


We use the following 10X Genomics kits and platforms for sequencing library preparation and sequencing.

  • Chromium Next GEM Single cell 5’ Kit v2
  • Dual Index Kit TT Set A 96rxn
  • Chromium Next GEM Chip K Single cell kit, 16 rxn
  • Chromium Single Cell Mouse/Human BCR amplification Kit, 16rxn
  • Chromium Single Cell Mouse/Human TCR amplification Kit, 16rxn
  • NovaSeq6k-S4

Key Features

  • Immune Cell Profiling assay
  • 5’ Single cell gene expression analysis
  • High resolution immune functional characterization
  • Precise pathway analysis
  • Cell type compositionTHIRD-PARTY RESOURCES (multiple)

Third-Party Resources

Cell Ranger and Loupe Browser | Single cell data analysis and data visualization tools

The Loupe Browser is a desktop application that provides interactive visualization functionality to analyze data from different 10x Genomics solutions. Cell Ranger and Loupe Browser