Transition state dynamics during a stochastic fate choice. Transition state dynamics during a stochastic fate choice

A stochastic differentiation programme shows stepwise separation of cell fate, with initiation of cell-type specific gene expression coupled to global transcriptome changes shared by all cells. Overall design: Single cell transcriptomes of disaggregated mound cells were determined using the Fluidigm C1 system. An average of around 3 million reads were generated from each single cell library. We excluded seven cells (marked in Supplementary file Dd_Mound_RawCounts.csv) based on the following criteria: total number of reads was lower than 5 x 10^5, percentage of mitochondrial reads was higher than 15%, or the data was missing a contiguous part of the transcriptome. We obtained a total of 116 cells, from 3 experimental replicates.

本随机分化程序可实现细胞命运的逐步分离，伴随细胞类型特异性基因表达的启动，且该过程同步发生所有细胞共有的全局转录组改变。实验整体设计：采用Fluidigm C1系统对解离后的丘状细胞进行单细胞转录组分析，每个单细胞文库平均生成约300万条reads。基于以下标准剔除7个细胞（标注于补充文件Dd_Mound_RawCounts.csv中）：总reads数低于5×10^5、线粒体reads占比高于15%，或转录组存在连续区域缺失。最终共获得来自3次生物学重复的116个有效细胞。