Single cell RNA sequencing identifies CXADR as a fate determinant of the placental exchange surface.

Tissue formation depends on adequate progenitor cell pool expansion followed by appropriate lineage specification events. Failures in these steps lead to anatomical defects that can have detrimental consequences, in particular when they occur during in utero development. Here, we subjected mouse trophoblast stem cells (TSCs) to targeted differentiation protocols to recapitulate the earliest steps in placenta formation, and followed the early lineage differentiation events by single cell sequencing approaches. In vitro differentiation of mouse TSCs was induced by inhibition of MEK with PD0325901 (2µM Final) (Inhibit dataset) or withdrawal of the stemness-maintaining components FGF4 and embryonic fibroblast conditioned medium (Remove dataset). Samples were collected at t0 (stem cell state, n=2), 1h (n=4 Inhibit and Remove), 4h (n=4 Inhibit and n=3 Remove), 24h (n=4 Inhibit and n=2 Remove), 36h (n=4 Inhibit and Remove) and 48h (n=4 Inhibit and Remove). Cells were dissociated and single cell barcoded transcriptome libraries were generated using Drop-Seq. Libraries were sequenced across multiple lanes of Illumina Nextseq, HiSeq2500 and HiSeq4000 flow cells in 6 batches.