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

Single Cell Gene Expression dataset analyzed using Cell Ranger 6.0.0

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Dataset overview

Output and supplemental files

Input files

Learn about Chromium analysis

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

The sample was run with intron mode. Libraries generated from neuronal nuclei typically have higher levels of reads mapped antisense to genes.

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: 20,982 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: 5,973
Median Genes per Cell: 1,843
Median UMI Counts per Cell: 3,706

This dataset is licensed under the Creative Commons Attribution license.