Extended Data Fig. 1: Further characterization of multiomic data.
From: Spatial multiomic landscape of the human placenta at molecular resolution
a, snRNA-seq quality control metrics, separated by samples. Left: number of genes detected per cell (Gex_nGenes) for each sample. Right: unique molecular identifiers per cell (Gex_nUMI) for each sample. Further QC metrics can be found in Supplementary Table 1. b, snATAC-seq quality control metrics showing TSS Enrichment scores and fragment counts per cell across all samples. c, UMAP plot showing cell origins (maternal origin or fetal origin) (Methods). d–e, UMAP plots (d) and dot plot (e) showing selected canonical marker genes expressed across main placental cell types including vCTB (PAGE4, PEG10), vCTBp (MKI67, TOP2A), EVT (HLA-G, CCNE1), STB (CYP19A1, ERVFRD-1), Endo (PECAM1, KDR), MAC (CD14, SPP1), and FIB (COL3A1, COL6A2). Further resolved clusters included vCTB1 (TBL1X), vCTB2 (SMAGP, IFI6), vCTB3 (LRP5), FIB1 (PDGFR1B, AGTR1), FIB2 (PDGFRA, CXCL14), Unknown 1 (Unk. 1) (HGF, DCN), mat. FIB (ALDH1A2, FAM155A), and Unknown 2 (Unk. 2) (PDN4, RSPO3). Manual sub-clustering revealed EVT1 (UTRN), EVT2, (HAPLN3, LY6E), EVT3 (AOC1, PAPPA2), mat. MAC (CD74, LYZ), HBC (LYVE1, ADAMTS17), and myeloid_unknown (myel. Unk) (GNA12, FGF13). f, Bar plot showing time point/donor composition per cluster. g, Myeloid cells further subclustered by Louvain clustering colored by sample. Maternal macrophages: mat. MAC, Hofbauer cells: HBC, and myeloid_unknown: myel. Unk. h, EVTs further subclustered by Louvain clustering colored by sample. i, Myeloid cells further subclustered by Louvain clustering colored by subcluster identity. j, EVTs further subclustered by louvain clustering colored by subcluster identity. k, STARmap-ISH (n = 3) characterization of trophoblast markers EGFR (pan-trophoblast), SMAGP (vCTB2), and LY6E (EVT) in sample W7-2. Stippled line demarcates the villous core from the vCTB layers. l, Gene expression patterns for novel motility and immunotolerance-promoting genes expressed in EVTs (PLXNB2, RUNX1, C12orf75, QSOX1, RASGRF2, PDCD1LG2, JAK1, MYCN, CD276, EBI3, FGFR1) and STBs (BRAF, TBX3) via UMAP visualization, with accompanying spatial visualization of FGFR1 using STARmap-ISH (n = 3). Stippled lines demarcate the villous core from vCTB layers. m, Heatmap showing novel differentially expressed genes across clusters. All differentially expressed genes from snRNA-seq can be found in Supplementary Table 2.
