EPI-Clone dataset: 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: Two where HSCs were clonally labeled with the LARRY system, transplanted to recipient mouse and profiled 4-5 months later (post-transplant hematopoiesis), and one where 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 mousePseudotime: Differentiation pseudotimePerformanceNonHhaI: Performance of the control amplicons in that cell