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. 2020 May 14;181(4):922–935.e21. doi: 10.1016/j.cell.2020.03.055

Figure S5.

Figure S5

Validation of the Spatial Mapping of Single-Cell Gene Expression Profiles, Related to Figure 4

(A) Whole mount in situ hybridization of expression profiles of Macho1 and Fkh at 4- to 64-cells stages.

(B) Whole mount in situ hybridization of expression profiles of FoxD-a/b and ZicL at 16- to 64-cells stages.

(C) Whole mount in situ hybridization of expression profiles of Wnt3 and AP-2-like2 at 16- to 64-cells stages.

(D) Whole mount in situ hybridization of expression profiles of Tbx6b at 4- to 16-cells stages.

(E) Whole mount in situ hybridization of expression profiles of TTF1, MyoD and Nodal at late 16-cells, late 32-cells and 64-cells stages (vegetal poles are shown unless indicated.

(F) Cell identity of cells expressing TTF1, MyoD and Nodal represented in segmented embryos. Vegetal and animal indicate the hemisphere view of the embryo.

(G) Expression levels of maternal factors asymmetrically inherited in the germ cell lineage (cells B3, B4.1 and B5.2) as measured by scRNA-Seq in Phallusia mammillata and Ciona robusta (Ciona robusta data is from Treen et al., 2018). All these factors are known to be asymmetrically partitioned from 4-cell stage onward (and 16-cell stage for DEAD-1) in Ciona robusta (Sardet et al., 2005). Phallusia gene IDs are identical to the ones from http://digitalembryo.org.

(H) Expression levels of marker genes in 16-cell stage cells as measured by scRNA-Seq in Phallusia mammillata and Ciona robusta (Ciona robusta data is from Treen et al., 2018). Tbx6b was not detected in Ciona robusta by scRNA-Seq by Treen et al. (2018) although Treen et al. (2018) could detect it by qPCR in embryos and by whole mount in situ hybridization in B5.1 cells. Phallusia gene IDs are identical to the ones from http://digitalembryo.org.

(I, J) Expression levels of CyclinB3 and HesA in 4- to 16-cell stage cells as measured by scRNA-Seq in Phallusia mammillata (I) and Ciona robusta (J) (Ciona robusta data is from Treen et al., 2018, RPM: reads per million mapped reads, RPKM: reads per kilo base per million, n.d.: not detected).(K) Expression levels of the forkhead transcription factor Fkh (FoxA) in 16-cell stage cells of Ciona robusta (Ciona robusta data is from Treen et al., 2018, n.d.: not detected).