Using this approach, we identified 30 lincRNAs whose knockdown produced expression patterns similar to differentiation into specific lineages (Supplemental Table 11). Amongst these lincRNAs, 13 are associated with endoderm differentiation, 7 with ectoderm differentiation, 5 with neuroectoderm differentiation, 7 with mesoderm differentiation, and 2 with the trophectoderm lineage (Figure 3a). Consistent with these functional assignments, we observe that the majority (>85%) of the 30 lincRNAs associated with specific differentiation lineages showed upregulation of the well-known marker genes for the identified states17,32 upon knockdown (such as Sox17 (endoderm), Fgf5 (ectoderm), Pax6 (neuroectoderm), Brachyury (mesoderm), and Cdx2 (trophectoderm)) (Figure 3b, Supplemental Figures 8, 9, Supplemental Tables 12, 13).
