This dataset is part of the Characterization of the tumor microenvironment Application Note.
A fresh surgical resection of a squamous non-small cell lung carcinoma tumor was obtained by 10x Genomics. Cells were sorted for live cells prior to running.
Gene expression, TCR Amplified, and BCR Amplified libraries were generated from about 15,000 cells (expected cell recovery 9,000) as described in the Single Cell V(D)J Reagent Kits User Guide (CG000086 Rev C) and sequenced on the Illumina NovaSeq 6000.
These libraries were analyzed using the Cell Ranger multi pipeline, which combines Gene Expression, Cell Surface Protein/Immune Receptor Mapping, TCR Amplified, and BCR Amplified libraries from the same sample. Cell Ranger multi enables consistent cell calling between gene expression and V(D)J libraries.
Sequencing Configuration
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Gene Expression: Paired-end (150x150), single-indexed sequencing. Read 1: 150 cycles, i7 index: 8 cycles, i5 index: 0 cycles, Read 2: 150 cycles.
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TCR Amplified: Paired-end (150x150), single-indexed sequencing. Read 1: 150 cycles, i7 index: 8 cycles, i5 index: 0 cycles, Read 2: 150 cycles.
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BCR Amplified: Paired-end (150x150), single-indexed sequencing. Read 1: 150 cycles, i7 index: 8 cycles, i5 index: 0 cycles, Read 2: 150 cycles.