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Human Jejunum 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

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Learn about Chromium analysis

Mouse jejunum 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.