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PBMCs from C57BL/6 mice (Next GEM v1.1)

Universal 5' Gene Expression dataset analyzed using Cell Ranger 3.1.0

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Mouse peripheral blood mononuclear cells (PBMCs) pooled from C57BL/6 mice were obtained from C&M LabPro (part number 11121911). The cells were 84% viable (trypan blue stain).

Amplified cDNA were used to generate 5’ gene expression, TCR enriched libraries, and Ig enriched libraries, following the Chromium Next GEM Single Cell V(D)J Reagent Kits v1.1 User Guide with Feature Barcode technology for Cell Surface Protein (CG000208).

The libraries were sequenced on an Illumina NovaSeq 6000 (NovaSeq software v1.6).

5’ Gene Expression

  • Sequencing Depth: 5’ Gene Expression Library - 70,665 read pairs per cell
  • Sequencing Coverage: Read 1 - 28 bp i7 Sample Index - 8 bp i5 Sample Index - 0 Read 2 - 91 bp

The key cell metrics were:

  • Cells detected - 10,982
  • UMI counts - 5,002
  • Median genes per cell - 1,726

V(D)J Enriched Libraries

TCR Libraries

  • Sequencing Depth: TCR Library - 40,043 read pairs per cell
  • Sequencing Coverage: Read 1 - 26 bp i7 Index - 8 bp i5 Index - 0 Read 2 - 91 bp

The key cell metrics were:

  • Cells detected - 1,077
  • Reads mapped to any V(D)J gene - 52.4%
  • Cells with productive V-J spanning pair - 71.1%

Ig Libraries

  • Sequencing Depth: Ig Library - 18,296
  • Sequencing Coverage: Read 1 - 26 bp i7 Sample Index - 8 bp i5 Sample Index - 0 Read 2 - 91 bp

The key cell metrics were:

  • Cells detected - 5,187
  • Reads mapped to any V(D)J gene - 90.6%
  • Cells with productive V-J spanning pair - 95.5%

This dataset is licensed under the Creative Commons Attribution license.