EPI-Clone supplementary dataset: Single cell RNA-seq of clonally barcoded hematopoietic progenitors

This is the dataset supporting the EPI-Clone manuscript: scRNA-seq profiling of hematopoietic stem and progenitor cells (HSPCs) was performed with the 3' 10x Genomics profiling. 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. Dataset is a seurat (v4) object with the following assays, reductions and metadata: ASSAYS: AB: Antibody expression data RNA: RNA expression profiles integrated: Integration of DNA methylation data performed across experimental batches with two batch correction methods: CCA (https://satijalab.org/seurat/reference/runcca) and harmony (https://portals.broadinstitute.org/harmony/articles/quickstart.html). DIMENSIONALITY REDUCTION pca_cca: PCA performed on the integrated data (CCA integration) umap_cca: UMAP computed on the integrated data (CCA integration) umap_harmony: UMAP computed on the integrated data (Harmony integration) METADATA 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 annotation LARRY: Error corrected LARRY barcode percent.mt: percentage of mitochondrial DNA nCount_RNA: Read count for the RNA modality nFeature_RNA: Number of RNAs with at least one read nCount_AB: Read count for the surface protein modality nFeature_AB: Number of ABs with at least one read