Human dissociated lymph node tumor cells of a 19-year-old male Hodgkin’s Lymphoma patient were obtained by 10x Genomics from Discovery Life Sciences. Whole transcriptome libraries were generated with Chromium Next GEM Single Cell 3' Reagent Kits v3.1 (Dual Index) User Guide (CG000315) and sequenced on an Illumina NovaSeq 6000.
Single Cell 3' Gene Expression v3.1 Dual Index Library
This whole transcriptome library was used as the parent library for downstream target enrichment (see additional datasets).
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Sequencing Depth: 78,314 mean reads per cell
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Paired-end (28 x 91)Read 1: 28 cycles (16 bp barcode, 12 bp UMI) i7 index: 10 cyclesi5 index: 10 cycles Read 2: 90 cycles (transcript read)
Note: To enable sample pooling with other 10x samples, the Illumina sequencers was run with a 91 bp R2 and trimmed in silico using the flag --r2-length=90.
Key metrics were:
- Cells targeted: 5,000
- Cells detected (whole transcriptome analysis): 3,394
- Median genes per cell: 1,696
- Median UMIs per cell: 5,890
- Sequencing saturation: 80.2%