Single-cell transcriptomic interrogation of hematopoietic progenitors within the E11.5 AGM of the mouse

To clarify the relationship between eMPPs and other progenitors, including pre-HSCs, within the AGM landscape, we performed single cell RNA-sequencing of hematopoietic progenitors within the E11.5 AGM. Overall design: Three Bl6 E11.5 embryos, pooled, were used for the single-cell experiment. Three populations were sorted: AGM pre-HSCs and endothelial cells (Lin- cKit+ CD45lo/mid CD31+ VE-Cad+); AGM progenitors (Lin- cKit+ CD45+); and fetal liver progenitors (cKit+/high CD45+ CD41- and cKit+/high CD45+ CD41high were separately sorted and mixed before encapsulation). Lineage markers used here were Ter119, Gr1, CD19, and CD3. Single-cell encapsulation was performed using 10X Chromium single cell 3' technology. Whole-transcriptome libraries were prepared using the 10X v3 protocol and sequenced on Illumina NextSeq500 paired-end 150 cycles (Read 1: 28 cycles; Index Read 1 (i7): 8 cycles; Read 2: 91 cycles).