Flash-Frozen Lymph Node with B Cell Lymphoma (14k sorted nuclei)

Flash-frozen intra-abdominal lymph node tumor from a patient diagnosed with diffuse small lymphocytic lymphoma of the lymph node was acquired from BioIVT Asterand®.

Nuclei were isolated from tiny pieces of the flash-frozen tumor lymph node following the Nuclei Isolation from Complex Tissues for Single Cell Multiome ATAC + Gene Expression Sequencing demonstrated protocol (CG000375). The isolated nuclei were stained with 7-AAD and then flow sorted using the BD FACSMelody™ cell sorter to clean up the nuclei from the debris. The 7-AAD positive sorted nuclei were then permeabilized using lysis buffer containing digitonin as per the demonstrated protocol.

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 v1.5 (Reverse Complement Strand Dual-Index Workflow). Nuclei loading was aimed for 15,000 recovery in expectation of overcounting after FACS sorting.

This dataset was highlighted in this Data Spotlight. Download the manually annotated Loupe file here.

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 v1.5 (Reverse Complement Strand Dual-Index Workflow)
• Cycle numbers:
  • Gene Expression library: 28,10,10,90
  • ATAC library: 50,8,24,49

Key metrics:

• Estimated number of cells: 14,566
• ATAC Mean raw read pairs per cell: 32,248
• ATAC Median high-quality fragments per cell: 8,396
• ATAC Number of peaks: 109,789
• GEX Mean raw reads per cell: 25,917
• GEX Median genes per cell: 1,186
• GEX Median UMI counts per cell: 1,671
• Linked genes: 12,382
• Linked peaks: 58,474

This dataset is licensed under the Creative Commons Attribution license.