GSE105267
Expression data of endothelium and hematopoietic cluster cells in the wild type and Steel mutant E11.5 AGM and vitelline and umbilical arteries
Kit ligand (Kitl, aka SCF) is a pivotal cytokine in fetal liver and bone marrow hematopoiesis. Its role in pre-liver embryonic hematopoiesis, however, is less well understood. We investigated the hematopoietic phenotype of Steel (Sl/Sl) mutant embryos, which lack Kitl, and found that the normal development of the HSC lineage in the aorta-gonad-mesonephros (AGM) region is negatively affected. We isolated endothelium and hematopoietic cluster cells from wild type and Sl/Sl AGM and vitelline and umbilical arteries for expression analysis by RNA-seq to investigate molecular changes in the developing HSC lineage and endothelial cells in the aortic HSC niche. Overall design: AGM and vitelline and umbilical arteries were dissected from E11.5 wild type and Sl/Sl mouse embryos, pooled according to genotype, and sorted into Ter119- VE-Cadherin+ c-Kit- CD41- CD45- endothelial cells and Ter119- VE-Cadherin+ c-Kit+ hematopoietic cluster cells by flow cytometry. Two biological replicates per cell type passed all quality controls and were used for analysis. Each replicate contained 100 sorted cells. Each replicate was paired end sequenced across 3 lanes, creating 6 fastq files per sample replicate. cDNA synthesis and library preparation were performed by the Single Cell core facility at the MRC Weatherall Institute of Molecular Medicine (Oxford, UK).