Derivation and functional annotation of human hematopoietic subpopulations from single-cell DNA methylation data

We report the development of a bisulfite based whole genome protocol suitable for use on single index sorted primary mammalian cells. Application of this protocol to murine and human hematopoietic stem cells provided quantitative DNA methylation measurements of up to 5.7 million CpGs in a single cell. To analyze the resulting datasets we developed a novel analytical approach designed to detect differences at single CpG resolution and identified epigenetically distinct subpopulations within the highly purified and functionally defined stem and progenitor populations. In silico merging of the methylation states from the single cells residing in each subpopulation allowed us to ascribe functional pathways to these epigenetically distinct subpopulations on the basis of their unique epigenetic states. Single-cell DNA methylation analysis of the heterogeneity within human primary hematopoetic stem cells RAW DATA was not provided. The lab will be submitting the sequencing data to EGA (https://www.ebi.ac.uk/ega/home).