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1k 1:1 Mixture of Human HEK293T and Mouse NIH3T3 Cells, Single Indexed

Single Cell Gene Expression dataset analyzed using Cell Ranger 4.0.0

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1:1 mixture of fresh frozen human HEK293T and mouse NIH3T3, cells obtained by 10x Genomics from ATCC, were used in a classic experiment to demonstrate single cell behavior. The same cells were used to generate Chromium Single Cell 3’ (Dual Index) data.

Libraries were prepared following the Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 User Guide (CG000204) and sequenced on Illumina NovaSeq 6000.

Single Cell 3’ Gene Expression v3.1 Single Index Library

  • Sequencing Depth: 139,675 read pairs per cell

  • Paired-end, single indexing Read 1: 28 cycles (16 bp barcode, 12 bp UMI) i7 index: 8 cycles (sample index) Read 2: 91 cycles (transcript)

  • Analysis Parameters Used: Run with --expect-cells=1,000

Key metrics were:

  • Cells detected: 1,602
  • Median UMI counts per cell: 58,290 (Human), 58,923 (Mouse)
  • Median genes per cell: 7,509 (Human), 6,527 (Mouse)

This dataset is licensed under the Creative Commons Attribution license.