Mouse Brain Nuclei Isolated with Chromium Nuclei Isolation Kit, SaltyEZ Protocol, and 10x Complex Tissue DP (CT Sorted and CT Unsorted)
Single Cell Multiome ATAC + Gene Expression dataset analyzed using Cell Ranger ARC 2.0.2
Learn about Chromium analysis
Mouse brain nuclei from frozen mouse and human tissue were isolated using three methods:
- Chromium Nuclei Isolation kit
- Salty EZ custom protocol
- 10x Complex Tissue Demonstrated Protocol (CT sorted and CT unsorted). For each tissue type, ~25 mg of tissue is aliquoted for each method.
Multiome libraries were prepared following the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide (CG000338) using the Chromium X instrument, targeting 5000 nuclei loads. Libraries were sequenced on an Illumina NovaSeq 6000 instrument, targeting 20000 reads (clusters) per cell.
Sequencing configuration:
Gene Expression libraries, paired-end, dual-indexed
- 28 bp read 1 (Barcode and UMI)
- 10 bp i7 sample barcode
- 10 bp i5 sample barcode
- 90 bp read 2 (Transcript)
ATAC libraries, single-indexed
- 50 bp read 1 (DNA insert)
- 8 bp i7 sample barcode
- 24 bp i5 (Barcode)
- 49 bp read 2 (DNA insert)
Data were analyzed using Cell Ranger ARC v2.0.2 with intronic reads included in the analysis, presented in the Chromium Nuclei Isolation Kit: Data Highlights & Methods Comparison for Single Cell Multiome ATAC + Gene Expression Technical Note.
This dataset is licensed under the Creative Commons Attribution license.