We curated lineage marker gene sets from published work and publicly available sources17,32,63. We identified lineage marker genes as significantly upregulated using the differential expression criteria outlined above. We validated the expression of these lineage marker genes for a selected set of lineage marker genes using qPCR (as described above) after a 4-day infection. Specifically, we looked at the expression of FGF5 (ectoderm), Sox1 (neuroectoderm), Sox17 (endoderm), Brachyury (mesoderm), and Cdx2 (trophectoderm). Primer sequences are listed in Supplemental Table 9. Expression estimates were normalized to Gapdh and compared to a panel of 25 negative control hairpins.
