Extended Data Table 1 Statistics of existing bacterial scRNA-seq methods

From: Single-cell massively-parallel multiplexed microbial sequencing (M3-seq) identifies rare bacterial populations and profiles phage infection

  1. Individual run statistics from previous studies of single-cell RNA-sequencing in bacteria. Numbers in each category were selected by taking maximum reported values. ‘Cells profiled’ indicates the maximum number of bacterial cells (for any number of strains) used in a single experiment. While ultimately the limiting factor is cost per cell, all else being equal, removing rRNA reads, either by using probes or rRNA depletion, will be more cost effective, with the latter also allowing for observation of unbiased gene sets. ‘Measurable genes’ indicates the number of genes that could theoretically be measured using the indicated method. ‘Median mRNA UMIs per cell’ indicates the maximum number of UMIs per mRNA per cell (for any number of strains and conditions) reported in the indicated study. ‘Median mRNA genes per cell’ same as ‘Median mRNA UMIs per cell’ except for genes. ‘Conditions profiled’ refers to the maximum number of reported samples/conditions profiled in a single experiment. While the limiting factor in conditions profiled is time and cost, we note that indexing multiple samples using indexed primers is currently the most time and cost efficient approach to profile multiple conditions.
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