Flexible experimental designs for valid single-cell RNA-sequencing experiments allowing batch effects correction

摘要

The hierarchical structure of the BUSseq model. Only in the gray rectangle is observed. A confounded design that contains three batches. Each polychrome rectangle represents one batch of scRNA-seq data with genes in rows and cells in columns; and each color indicates a cell type. Batch 1 assays cells from cell types 1 and 2; batch 2 profiles cells from cell types 3 and 4; and batch 3 only contains cells from cell type 4. The complete setting design. Each batch assays cells from all of the four cell types, although the cellular compositions vary across batches. The reference panel design. Batch 1 contains cells from all of the cell types, and all of the other batches have at least two cell types. The chain-type design. Every two consecutive batches share two cell types. Batch 1 and Batch 2 share cell types 2 and 3; Batch 2 and Batch 3 share cell types 3 and 4 (see also Supplementary Figs.  and ).