Extended Data Fig. 2: Regressing mitochondrial genes and normalizing UMI did not remove batch effects.
From: A multicenter study benchmarking single-cell RNA sequencing technologies using reference samples
Five different batches of scRNA-seq data (10X_LLU_A, 10X_LLU_B, 10X_NCI_A, 10X_NCI_B, and 10X_NCI_Mix5) generated at two sites (LLU and NCI) are shown either as t-SNE plots (panels a-d) or as UMAPs (panels e-h). (a) logNormalized, scaled data with no regression; (b) logNormalized, scaled data filtered with mitochondrial (Mito) gene regression >5% and UMI normalization by Seurat v3; (c) sctransform with no regression; (d) sctransform with mitochondrial gene regression and UMI normalization; (e) logNormalized, scaled data with no regression; (f) scaled data with mitochondrial gene regression and UMI normalization; (g) sctransform with no regression; and (h) sctransform with mitochondrial gene regression and UMI normalization.
