Single Cell HTAN SCLC

These data include a subset of single-cell samples from the CPTAC Glioblastoma data processed using the following steps:

Ensembl gene ID's were matched to HGNC symbols, chromosome name, starting position, and ending position via Biomart using the scater R package.

Size factors were computed using the scran R package.

UMAP dimensions were computed using the scater R package.

Probes without matching HGNC symbols were removed.

Where duplicate HGNC symbols were present, the gene with the maximum normalized range was retained.

Cell types were inferred using the scMRMA R package.

Cells with less than or equal to 1,000 features were removed.

Cells with mitochondrial reads greater than or equal to 50% were removed.

Expression data for each cell type were saved separately for each sample.

For macrophages for each sample, a differentiation trajectory was estimated using the monocle3 R package, and plots were colored by combined expression of the M0 markers CSF1R, CD14, CD68, and CD11B, the M1 markers CD86, MARC0, CXCL9, CXCL10, CXCL11, NOS2, SOCS1, and CD64, and the M2 markers TGM2, CD23, ARG1, CCL22, CD163, and CD206 (from PMC8268869). Pseudotime starting points were annotated in monocle3 using visual inspection of plots. Only samples in which a visible trajectory from M0 -> M1 -> M2 was evident using these markers were retained.

For B cells and T cells for each sample, a differentiation trajectory was estimated using the monocle3 R package, and plots were colored by combined expression of the B cell and T cell differentiation markers TCF3, FOXO1, EBF1, and PAX5 and TCF3, NOTCH1, HES1, TCF7, TLE3, TLE6, BCL11B, and GATA3, respectively (from PM24679436). Pseudotime starting points were annotated in monocle3 using visual inspection of plots. Only samples in which a visible trajectory of dedifferentiation was evident using these markers were retained.

For endothelial cells for each sample, a differentiation trajectory was estimated using the monocle3 R package, and plots were colored by combined expression of the endothelial cell differentiation markers GATA2, FLI1, SOX7, SOX18 (from PM28334937). Pseudotime starting points were annotated in monocle3 using visual inspection of plots. Only samples in which a visible trajectory of dedifferentiation was evident using these markers were retained.

For fibroblasts for each sample, a differentiation trajectory was estimated using the monocle3 R package, and plots were colored by combined expression of fibrogenesis markers TGFB1, FGF2, ANGPT1, ANGPT2, PDGFA, PDGFB, PDGFC, PDGFD, VEGFA, and VEGFB (from PM17280897). Pseudotime starting points were annotated in monocle3 using visual inspection of plots. Only samples in which a visible trajectory of dedifferentiation was evident using these markers were retained.

For NK cells for each sample, a differentiation trajectory was estimated using the monocle3 R package, and plots were colored by combined expression of transmembrane proteins that mediate cytotoxicity, FASLG and TNFSF10 (from PM31107565). Pseudotime starting points were annotated in monocle3 using visual inspection of plots. Only samples in which a visible trajectory of dedifferentiation was evident using these markers were retained. These pseudotime assignments (and other cell type assignments) are available from HTAN_SCLC_pseudotime.zip.

For all cell types for each sample, 5-fold cross-validation matrices for expression, PCA, and pseudotime were generated across 1 random split, for a total of 5 files per cell type, per sample. These files are available from HTAN_SCLC_expression.zip.