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. 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.