Cells from a combined cortex, hippocampus, and subventricular zone of an E18 mouse tissue were obtained by 10x Genomics from BrainBits LLC. 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 Illumina NovaSeq 6000.
Single Cell 3’ Gene Expression v3.1 Dual Index Library
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Sequencing Depth: 130,362 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: 10,920
- Median UMI counts per cell: 10,586
- Median genes per cell: 3,636