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10k Peripheral Blood Mononuclear Cells (PBMCs) from a Healthy Donor, Dual Indexed

Universal 3' Gene Expression dataset analyzed using Cell Ranger 4.0.0

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Learn about Chromium analysis

Peripheral blood mononuclear cells (PBMCs) from a healthy donor were obtained by 10x Genomics from AllCells. The same cells were used to generate Chromium Single Cell 3’ (Single Index) data.

Libraries were prepared following the Chromium Next GEM Single Cell 3ʹ 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: 110,728 read pairs per cell

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

  • Analysis Parameters Used: Run with --expect-cells=10,000

Key metrics were:

  • Cells detected: 10,915
  • Median UMI counts per cell: 8,504
  • Median genes per cell: 2,310

This dataset is licensed under the Creative Commons Attribution license.