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PBMCs from a Healthy Donor: Whole Transcriptome Analysis

Single Cell Gene Expression dataset analyzed using Cell Ranger 4.0.0

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Human peripheral blood mononuclear cells (PBMCs) of a healthy female donor aged 25 were obtained by 10x Genomics from AllCells. Whole transcriptome libraries were generated with Chromium Next GEM Single Cell 3' Reagent Kits v3.1 (Dual Index) User Guide (CG000315) and sequenced on an Illumina NovaSeq 6000.

Single Cell 3' Gene Expression v3.1 Dual Index Library

  • Sequencing Depth: 69,859 reads pairs per cell

  • Paired-end (28 X 91), dual-indexing Read 1: 28 cycles (16 bp barcode, 12 bp UMI) i7 index: 10 cycles i5 index: 10 cycles Read 2: 90 cycles (transcript)

Note: To enable sample pooling with other 10x samples, the Illumina sequencer was run with a 91 bp R2 and trimmed in silico using the flag -r2-length=90.

Key metrics were:

  • Cells targeted: 10,000
  • Cells detected (whole transcriptome analysis): 10,194
  • Median genes per cell: 2,152
  • Median UMI per cell: 7,697
  • Sequencing saturation: 74.1 %

This dataset is licensed under the Creative Commons Attribution license.