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10k Human PBMCs, 3' v3.1, Chromium X (with intronic reads)

Universal 3' Gene Expression dataset analyzed using Cell Ranger 6.1.2

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Learn about Chromium analysis

Human peripheral blood mononuclear cells (PBMCs) of a healthy female donor aged 25-30 were obtained by 10x Genomics from AllCells.

Libraries were generated from ~16,000 cells (11,984 cells recovered) as described in the Chromium Single Cell 3' Reagent Kits User Guide (v3.1 Chemistry Dual Index) (CG000315 Rev C) using the Chromium X and sequenced on an Illumina NovaSeq 6000 to a read depth of approximately 40,000 mean reads 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: --expect-cells=10000 and --include-introns

This dataset is licensed under the Creative Commons Attribution license.