Fresh Embryonic E18 Mouse Brain (5k)
Epi Multiome ATAC + Gene Expression dataset analyzed using Cell Ranger ARC 2.0.0
Learn about Chromium analysis
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: 4,878
- ATAC Mean raw read pairs per cell: 39,755
- ATAC Median high-quality fragments per cell: 16,446
- ATAC Number of peaks: 172,193
- GEX Mean raw reads per cell: 97,172
- GEX Median genes per cell: 3,120
- GEX Median UMI counts per cell: 7,984
- Linked genes: 10,481
- Linked peaks: 56,250
This dataset is licensed under the Creative Commons Attribution license.