SCEED – design and analysis of single cell RNA-seq experiments for cell type identification

The advent of single cell RNA sequencing (scRNA-seq) enabled researchers to study transcriptomic activity within individual cells and identify inherent cell types in the sample. Although numerous computational tools have been developed to analyze single cell transcriptomes, there are no published studies and analytical packages available to guide experimental design and to devise suitable analysis procedure for cell type identification.

Researchers from the Jackson Laboratory for Genomic Medicine have developed an empirical methodology to address this important gap in single cell experimental design and analysis into an easy-to-use tool called SCEED (Single Cell Empirical Experimental Design and analysis). With SCEED, user can choose a variety of combinations of tools for analysis, conduct performance analysis of analytical procedures and choose the best procedure, and estimate sample size (number of cells to be profiled) required for a given analytical procedure at varying levels of cell type rarity and other experimental parameters. Using SCEED, the researchers examined 3 single cell algorithms using 48 simulated single cell datasets that were generated for varying number of cell types and their proportions, number of genes expressed per cell, number of marker genes and their fold change, and number of single cells successfully profiled in the experiment.

Schematic representation showing generation of simulated dataset using SCEED


(Left to right) A blank matrix is provided as an input where initially (1) mean expression of all the genes and (2) number of marker genes at a desired foldchange cutoff are simulated, followed by adjustment of (3) biological and (4) technical noises. Finally, (5) single cell count is simulated and provided as an output matrix

Based on this study, the researchers found that when marker genes are expressed at fold change of 4 or more, either Seurat or SIMLR algorithm can be used to analyze single cell dataset for any number of single cells isolated (minimum 1000 single cells were tested). However, when marker genes are expected to be only up to fold change of 2, choice of the single cell algorithm is dependent on the number of single cells isolated and rarity of cell types to be identified. In conclusion, this work allows the assessment of various single cell methods and also aids in the design of single cell experiments.

Abrams D, Kumar P, Karuturi RKM, George J. (2019) A computational method to aid the design and analysis of single cell RNA-seq experiments for cell type identification. BMC Bioinformatics 20(Suppl 11):275. [article]

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