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All raw sequencing datasets (RNA-seq, ChIP-seq and scRNA-seq) that support the findings of this study have been deposited to GEO repository (hosted by NCBI) under the superseries identifier GEO: GSE127937. Subseries numbers are for each experiment set and data type: RNA-Seq: BMP4 time-course (Figures 2 and and3) =3) = GEO: GSE127936; RNA-Seq: TROPH/ENDO/MESO lineage time-courses (Figure 6) = GEO: GSE127935; ChIP-Seq: SMAD1 ChIP Seq in H1 cells (Figure 2) = GEO: GSE135254; ChIP-Seq: GATA3 ChIP Seq in H1 cells (Figure 5) = GEO: GSE135255; scRNA-Seq: 48 hr BMP4 in wt and GATA3 KO cells (Figure S7) = GEO: GSE135253
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