Massively-parallel Microbial mRNA Sequencing (M3-Seq) reveals heterogenous behaviors in bacteria at single-cell resolution

M3-Seq is a single-cell RNA-sequencing platform for bacteria that pairs combinatorial cell indexing with post hoc rRNA depletion. We use M3-Seq to profile hundreds of thousands of bacterial cells and reveal rare populations of bacteria that include bet-hedging strategies, prophage induction, and phage-infected cells in E. coli and B. subtilis. Bacterial cells were grown and treated as described in the M3-Seq manuscript. Each named experiment corresponds to a different dataset.

M3-Seq是一款面向细菌的单细胞RNA测序（single-cell RNA-sequencing）平台，该平台将组合式细胞索引与事后核糖体RNA耗竭技术相结合。我们依托该平台对数十万细菌细胞开展转录组表征分析，成功揭示了大肠杆菌（E. coli）与枯草芽孢杆菌（B. subtilis）中存在的稀有细菌种群，这些种群涵盖风险对冲生存策略、原噬菌体诱导以及噬菌体感染细胞等关键表型特征。细菌细胞的培养与处理严格参照M3-Seq相关研究论文中的实验流程完成。每个命名实验均对应一个独立的数据集。