Probe barcode-associated technical variation in probe-based single-cell RNA sequencing: data objects

Data objects supporting the analysis of probe barcode-associated technical variation in 10x Genomics Flex (probe-based) single-cell RNA sequencing. When cells from the same population are split across probe barcodes, differential expression analysis reveals a substantial number of spurious differentially expressed genes driven by probe barcode identity rather than biology. These objects support analyses quantifying and mechanistically investigating this artifact, and comparing its magnitude between Flex v1 and Flex v2. Included files: seurat_A375_flexv2_filtered.qs: Seurat object (v5) containing A375 melanoma cells processed with the 10x Genomics Flex v2 single-cell RNA-seq protocol. Cells are labeled by probe barcode identity in the metadata column probe_barcode. Gene expression is stored as normalized counts in the default RNA assay. Load with qs::qread(); requires Seurat >= 5.0 and qs >= 0.25. vcc_probe_expr_sparse_cache_10k_feat_filt.rds: Sparse matrix cache of per-probe (not per-gene) expression values for Virtual Cell Challenge (VCC) cells processed with Flex v1. A list with $data (dgCMatrix; rows = probe IDs, columns = cells) and $barcodes (probe barcode assignment per cell). Probe IDs follow the format ENSGXXXXXXXX-GENENAME-xxxxxxx. Load with readRDS(); requires Matrix >= 1.5. flex_v2_probe_expr_sparse_cache_10k_feat_filt.rds: Sparse matrix cache of per-probe expression values for A375 melanoma cells processed with Flex v2. Same structure as the VCC cache above. Used to assess whether probe barcode-associated artifacts observed in Flex v1 are reduced in the updated kit. Load with readRDS(); requires Matrix >= 1.5.