Extended Data Fig. 1: Technical information about scRNA-seq library and overview of haematopoietic clusters.
From: Deciphering human macrophage development at single-cell resolution
a, Graph showing distribution of UMI per cell for STRT–seq data (n = 8 biologically independent embryo samples and 1,461 cells). Threshold for final analysis was set at >10,000. b, Percentage of UMIs mapped on to ERCC and average expression of house-keeping genes. nGene: number of genes expressed, nUMI: number of UMIs expressed. c, UMAP visualization showing exclusion of non-haematopoietic cells from final analysis based on expression of PTPRC, EPCAM, KRT8 and COL1A1. d, Numbers, ___location and Carnegie stage information for cells used in final analysis. e, UMAP showing minimal batch effect among single cell libraries (n = 1,231 cells). f, g, UMAP visualization of all haematopoietic cells with Carnegie stage (f) and site (g) information mapped on. h, Violin plots of average gene and UMI numbers of scRNA-seq in STRT–seq data. For box plot within each violin plot, centre black lines indicate median values, boxes range from 25th to 75th percentiles, and whiskers correspond to 1.5× IQR. i, Gene and UMI numbers of identified haematopoietic clusters. Centre black lines indicate median values, boxes range from 25th to 75th percentiles, and whiskers correspond to 1.5× IQR. j, Heat map of the top five DEGs between haematopoietic clusters. DEGs were detected using FindAllMarkers function in Seurat (one-sided Wilcoxon rank-sum test, with P value adjusted for multiple testing using Bonferroni correction), and genes with fold change >1.5 and adjusted P < 0.05 were selected. k, GSEA plots of erythroid and myeloid signatures indicate significantly lower expression of erythroid signature in human YSMPs than in mouse EMPs (extracted from a published scRNA-seq dataset)19 (n = 70 human YSMP cells and 118 mouse EMP cells). P value was calculated using permutation test (one-sided) based on phenotype by GSEA 3.0 software, representing statistical significance of normalized enrichment score (NES). FDR, false discovery rate. l, Gene expression of haematopoietic progenitor feature (CD34, MYB), erythroid feature (GATA1, KLF1) and myeloid feature (SPI1, MPO, LYZ, CSF1R) in human YSMPs and mouse EMPs13,19.
