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5k Mouse E18 Combined Cortex, Hippocampus and Subventricular Zone Cells

Single Cell Gene Expression dataset analyzed using Cell Ranger 6.0.0

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Cells from a combined cortex, hippocampus, and subventricular zone of an E18 mouse tissue (C57BL/6 strain) were obtained by 10x Genomics from BrainBits LLC. The same cells were used to generate nuclei and as part of the multiplexed sample.

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

  • Sequencing Depth: 28,731 read pairs 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)

Key Metrics

  • Estimated Number of Cells: 5,483
  • Median Genes per Cell: 2,857
  • Median UMI Counts per Cell: 7,277

This dataset is licensed under the Creative Commons Attribution license.