EPI-Clone datasets M.1-M.3: Single cell targeted DNA methylation profiling of hematopoietic stem and progenitor cells

This is the dataset supporting the EPI-Clone manuscript: Targeted single cell methylation profiling of hematopoietic stem and progenitor cells (HSPCs) was performed with the scTAMseq method. Three experiments are included: In M.1 and M.2 HSCs were clonally labeled with the LARRY system, transplanted to recipient mouse and profiled 4-5 months later (post-transplant hematopoiesis). In M.3 HSPCs were profiled straight from an unperturbed mouse.<b>Remaining experiments are available under different DOIs:</b>Mature cell experiment: https://doi.org/10.6084/m9.figshare.25472467Unperturbed old vs young mouse experiment: https://doi.org/10.6084/m9.figshare.25472434Human total bone marrow: https://doi.org/10.6084/m9.figshare.25526899Dataset is a seurat (v4) object with the following assays, reductions and metadata:<br><b>ASSAYS:</b>AB: Antibody expression dataDNAm: DNA methylation data, containing binary observations (0: amplicon not observed, i.e. dropout or absence of DNA methylation, 1: amplicon observed, i.e. DNA methylation). See the paper on scTAMseqintegrated: Integration of DNA methylation data performed across experimental batches.<b>DIMENSIONALITY REDUCTION</b>pca: PCA performed on the integrated dataumap: UMAP computed on the integrated dataFor strategies how to obtain dimensionality reduction that reflect clonal identity, please see the github page accompanying the manuscript.<b>METADATA</b>Experiment: The experiment that the cell is from, values are "LARRY main experiment", "LARRY replicate" and "Native hematopoiesis"ProcessingBatch: Experiments were processed in several batches.CellType: Cell type annotationLARRY: Error corrected LARRY barcodeLARRYSize: Size of the cloneGFP.or.Saphire: Identity of the donor mouse. For M.1, two donor mice were sacrificed and HSCs were labeled with LARRY constructs containing a GFP label in one case, and LARRY constructs containing a Sapphire label in the other case. Subsequently, labeled cells from each donor were transplanted into two recipient mice each. Accordingly, the data set contains cells from four mice that contain two sets of clones, labeled with GFP and Sapphire, respectively.Pseudotime: Differentiation pseudotimePerformanceNonHhaI: Performance of the control amplicons in that cell