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Aggregate of 8 Chromium Connect channels and 8 manual channels

Single Cell Gene Expression dataset analyzed using Cell Ranger 3.1.0

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PBMCs isolated and cryopreserved by AllCells. PBMCs are primary cells with relatively small amounts of RNA (~1pg RNA/cell). The same lot of PBMCs were used for both manual and Connect runs. 1 full chip (8 channels) was run manually and 1 full chip (8 channels) was run on the Chromium Connect. This aggregate is of those 16 samples. Peripheral blood mononuclear cells (PBMCs) from a healthy donor - Chromium Connect and Peripheral blood mononuclear cells (PBMCs) from a healthy donor - Manual are specific channels from this dataset.

Libraries were prepared following either the Chromium Single Cell 3ʹ Reagent Kits v3.1 User Guide (CG000204 RevD) or Chromium Next GEM Automated Single Cell 3ʹ Reagent Kits v3.1 (CG000286 RevA) on the Chromium Connect.

  • 5,000 cells targeted per channel

  • Sequenced on Illumina NovaSeq

  • 28bp read1 (16bp Chromium barcode and 12bp UMI), 91bp read2 (transcript), and 8bp I7 sample barcode

  • run with cellranger count using --expect-cells=5000

  • 66,457 cells detected

This dataset is licensed under the Creative Commons Attribution license.