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. Brain tissue was dissociated following the 10x Demonstrated Protocol for Dissociation of Mouse Embryonic Neural Tissue for Single Cell RNA Sequencing (CG00055).
Gene Expression libraries were generated as described in the Chromium Single Cell 3' Reagent Kits User Guide (v3.1 - Dual Index) User Guide (CG000315) and sequenced on an Illumina NovaSeq 6000 with approximately 80,000 read pairs per cell.
Paired-end, dual indexing:
- 28 cycles Read 1
- 10 cycles i7
- 10 cycles i5
- 90 cycles Read 2
The cellranger multi pipeline in Cell Ranger v8.0.0 was used to analyze libraries.