Extended Data Fig. 2: scRNA-seq and snRNA-seq data quality control and data analysis overview.
From: Spatial multiomics map of trophoblast development in early pregnancy
a: Overview of the computational pipeline implemented for analysis of in vivo scRNA-seq and snRNA-seq data. Data integrated with scVI. b–e: (top) UMAP (uniform manifold approximation and projection) scatterplots of donors P13 (n = 67,821 nuclei), P14 (n = 45,166 nuclei), Hrv43 (n = 60,837 nuclei and cells) and all donors’ (n = 325,665 nuclei and cells, m = 18 donors) scRNA-seq and snRNA-seq data (b-e respectively) for all recovered cell states, coloured by coarse grain compartment annotation and metadata labels: assay, sample (10X library), donor and developmental age. (bottom) Dot plots show normalised, log-transformed and variance-scaled expression of genes characteristic of coarse grain compartment (X-axis) in donors profiled (Y-axis). Single-cell RNA sequencing (scRNA-seq), single-nuclei RNA sequencing (snRNA-seq), maternal (m), fetal (f), natural killer (NK), innate lymphocytes (ILC), single-cell RNA sequencing (scRNA-seq), single-nuclei RNA sequencing (snRNA-seq).
