Mouse Brain Nuclei Isolated with Chromium Nuclei Isolation Kit, SaltyEZ Protocol, and 10x Complex Tissue DP (CT Sorted and CT Unsorted)

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.