Fresh cortex, hippocampus, and ventricular zone from embryonic mouse brain (E18) were obtained by 10x Genomics from BrainBits, LLC.
Nuclei were isolated as described in the Demonstrated Protocol- Nuclei Isolation from Mouse Brain Tissue for Single Cell Multiome ATAC + Gene Expression Sequencing (CG000366 Rev A).
Paired ATAC and Gene Expression libraries were generated from the isolated nuclei as described in the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide (CG000338 Rev A) and sequenced on Illumina Novaseq 6000 v1 Kit (Forward Strand Dual-Index Workflow).
User Guide: Chromium Next Gem Single Cell Multiome ATAC + Gene Expression User Guide (CG000338 Rev A)
Libraries generated:
- Chromium Single Cell Multiome ATAC library
- Chromium Single Cell Multiome Gene Expression library
Sequencing information:
- Sequencer: Novaseq 6000 v1 Kit (Forward Strand Dual-Index Workflow)
- Cycle numbers:
- Gene Expression library: 28,10,10,90
- ATAC library: 50,8,16,49
Key metrics:
- Estimated number of cells: 4,881
- ATAC Mean raw read pairs per cell: 39,730
- ATAC Median high-quality fragments per cell: 15,103
- ATAC Number of peaks: 144,437
- GEX Mean raw reads per cell: 97,111
- GEX Median genes per cell: 7,983
- GEX Median UMI counts per cell: 3,120
- Linked genes: 9,951
- Linked peaks: 48,735