Extended Data Fig. 3: Validation of STRT–seq macrophage clustering in yolk sac by 10x Genomics.
From: Deciphering human macrophage development at single-cell resolution
a, Quality control for 10x Genomics data by UMI and gene numbers (n = 2 biologically independent embryo samples and 11,944 cells). The threshold for final analysis was set as gene number >1,000 per cell. b, UMAP visualization of total haematopoietic clusters generated via STRT–seq with cells from yolk sac (n = 5 biologically independent embryo samples and 238 cells) mapped on and coloured by stage information, which were extracted for further analysis. c, PCA of cells from yolk sac in STRT–seq with re-clustering (left) and stage (right) information mapped on (n = 5 biologically independent embryo samples and 238 cells). These cells were re-clustered into three clusters and annotated by gene expression profiles. The YS-Mac1 cluster mainly consisted of cells from CS11, while the YS-Mac2 cluster mainly consisted of cells from CS15. Based on these findings, we selected the 10x Genomics data from the CS11 and CS15 yolk sacs to validate our clustering. d, UMAP visualization of 10x Genomics data from CS11 and CS15 yolk sacs (n = 2 biologically independent embryo samples and 9,565 cells). The Mac cluster was extracted for further analysis. e, PCA of Mac cluster in 10x Genomics data with re-clustering (left) and stage (right) information mapped on. f, Expression profile of top ten DEGs between YS-Mac1 and YS-Mac2 identified by STRT–seq (n = 238 cells) and projected onto the 10x Genomics data (n = 9,565 cells). Even though 10x Genomics data have lower depth compared to STRT–seq, similar expression profiles can be seen for the majority of genes. g, UMAP visualization of integrated yolk sac data from STRT–seq and 10x Genomics analysis (n = 9,803 cells). There is less overlap in the mesenchymal (Mes1 and Mes2) and epithelial (Epi1) clusters because the STRT–seq data were only from CD45+ haematopoietic cells, whereas the 10x Genomics data were from all yolk sac cells. Note that YSMPs from both datasets are well merged. h, Bar plot showing putative surface markers of YSMPs. On the basis of these data, CD34 and CD44 were selected for functional assays. DEGs were identified from combined STRT–seq and 10x Genomics data using FindAllMarkers function in Seurat (one-sided Wilcoxon rank-sum test with P value adjusted for multiple testing using Bonferroni correction), and surface marker genes with fold change >1.25 and adjusted P < 0.05 were selected.
