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’ (Single Index) data.
Libraries were prepared following the Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (Dual Index) User Guide (CG000315) and and sequenced on Illumina NovaSeq 6000.
Single Cell 3’ Gene Expression v3.1 Dual Index Library
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Sequencing Depth: 126,588 read pairs per cell
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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)
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Analysis Parameters Used: Run with --expect-cells=10,000
Key metrics were:
- Cells detected: 12,721
- Median UMI counts per cell: 45,238 (Human), 54,852 (Mouse)
- Median genes per cell: 6,824 (Human), 6,371 (Mouse)