NSCLC tumor - 5’ gene expression
Single Cell Immune Profiling dataset analyzed using Cell Ranger 2.2.0
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Dataset overview
Output and supplemental files
Input files
Learn about Chromium analysis
5’ gene expression data from a fresh surgical resection of a squamous non-small cell lung carcinoma tumor.
The same cDNA was used to generate TCR (vdj_v1_hs_nsclc_t) 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
- ~9,000 expected cells recovered (based on cell viability* and capture efficiency)
- 7,802 cells detected
- 1,442 median genes per cell and 4,197 median UMI counts per cell detected
- Sequenced on an Illumina NovaSeq 6000 with NovaSeq software v1.2 with ~48,000 read pairs per cell
- 150bp read1 (including 16bp Chromium barcode and 10bp UMI), 150bp read2 (transcript), and 8bp i7 sample barcode read configuration
- Analysis run with --force-cells=7802 (for explanation of the --force-cells parameter see the Calling Cell Barcodes section of the support page)
* viability assumed to be 100%. Cells were sorted for live cells but cell counts were not performed post sorting to minimize cell loss.
This dataset is licensed under the Creative Commons Attribution license.