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NSCLC tumor - TCR enrichment from amplified cDNA

Single Cell Immune Profiling dataset analyzed using Cell Ranger 2.2.0

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Targeted enrichment of TCRs from a fresh surgical resection of a squamous non-small cell lung carcinoma tumor.

The same cDNA was used to generate gene expression (vdj_v1_hs_nsclc_5gex) and B cell Ig (vdj_v1_hs_nsclc_b) specific libraries.

Libraries were prepared following the Single Cell V(D)J Reagent Kits User Guide (CG000086 Rev C).

  • ~15,000 cells loaded
  • 2,235 expected TCR-expressing cells recovered (based on CD3D/CD3E expressing fraction in the gene expression data)
  • 2,012 cells detected with either single TRA or TRB or both
  • 1,538 cells with productive V-J spanning (TRA, TRB) pair
  • Sequenced on an Illumina NovaSeq 6000 with NovaSeq software v1.2 with ~21,000 read pairs per cell
  • 150bp read1 (including 16bp Chromium barcode, 10bp UMI, 13bp switch oligo and transcript), 150bp read2 (transcript), and 8bp i7 sample barcode read configuration

This dataset is licensed under the Creative Commons Attribution license.