Orthologous genes among three species

For the cross‐species comparison analyses for SC3‐seq and 10X scRNA‐seq data, we retrieved the lists of orthologous genes among three species from Ensembl BioMart (Ensembl 97: Jul 2019) as shown in Dataset EV9. One‐to‐one (1–1) orthologous genes between human and cy (16,734 genes) were used for the cross‐species integration of SC3‐seq data. One‐to‐one‐to‐one (1–1–1) orthologous genes across three species (15,007 genes) were used for the cross‐species integration of 10X data. As the orthologous gene list from Ensembl BioMart was relatively incomplete, we made a genomic coordinate comparison list by using the LiftOver tool as previously described (Sasaki et al, 2015; Nakamura et al, 2016) (Dataset EV9).