Single-cell proteo-genomic reference maps of the human hematopoietic system

To establish a comprehensive single-cell transcriptomic and surface proteomic map of the human bone marrow (BM), we performed a series of Abseq experiments, in which mononuclear BM cells from hip aspirates were labelled with 97-197 oligo-tagged antibodies, followed by targeted or whole transcriptome scRNAseq on the Rhapsody platform. For targeted single-cell transcriptome profiling, we established a custom panel, consisting of 462 mRNAs covering all HSPC differentiation stages, cell type identity genes, mRNAs of surface receptors and additional genes that permit the characterization of cellular states. Using this panel, in combination with 97 surface markers, we analyzed the BM of three young healthy donors, and three aged healthy donors. This dataset serves as a reference dataset. The following additional datasets were created and are analysed in the context of the reference: - 97 antibodies & Whole Transcriptome Sequencing: Enables to query any gene’s expression in the space defined by our reference and serves to validate that the targeted mRNA sequencing approach does not lead to reduced resolution - 197 antibody & targeted mRNA profiling: Enables to query the expression of 100 additional antigens in the context of our reference - 15 AML patients profiled for 97 antibodies & targeted mRNA profiling: Illustrates how to interpret new data from diseased individuals in the context of the reference, see also https://git.embl.de/triana/nrn/-/tree/master/Projection_Vignette This project contains one Seurat objects for the 97-marker reference experiment, and one Seurat file for each additional dataset. The data can be browsed interactively at https://abseqapp.shiny.embl.de