After the single cell gene count matrix was generated, each cell was assigned to its original mouse embryo based on the RT barcode. Reads mapping to each embryo were aggregated to generate “bulk RNA-seq” for each embryo. For sex separation of embryos, we counted reads mapping to a female-specific non-coding RNA (Xist) or chrY genes (except Erdr1 which is in both chrX and chrY). Embryos were readily separated into females (more reads mapping to Xist than chrY genes) and males (more reads mapping to chrY genes than Xist).
Pseudotemporal ordering of whole mouse embryos was done by Monocle 257 . Briefly, an aggregated gene expression matrix was constructed as described above. Differentially expressed genes across different development conditions were identified with differentialGeneTest function of Monocle 257 . The top 2,000 genes with the lowest q value were used to construct the pseudotime trajectory using Monocle 257 . Each embryo was assigned a pseudotime value based on its position along the trajectory.
Pseudotemporal ordering of whole mouse embryos was done by Monocle 257 . Briefly, an aggregated gene expression matrix was constructed as described above. Differentially expressed genes across different development conditions were identified with differentialGeneTest function of Monocle 257 . The top 2,000 genes with the lowest q value were used to construct the pseudotime trajectory using Monocle 257 . Each embryo was assigned a pseudotime value based on its position along the trajectory.
