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.<br>Dataset is a seurat (v4) object with the following assays, reductions and metadata:<b>ASSAYS:</b><br>AB: Antibody expression data<br>RNA: RNA expression profiles<br>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).<br><b>DIMENSIONALITY REDUCTION</b><br>pca_cca: PCA performed on the integrated data (CCA integration)<br>umap_cca: UMAP computed on the integrated data (CCA integration)<br>umap_harmony: UMAP computed on the integrated data (Harmony integration)<b>METADATA</b><br>Experiment: The experiment that the cell is from, values are "LARRY main experiment", "LARRY replicate" and "Native hematopoiesis"<br>ProcessingBatch: Experiments were processed in several batches.<br>CellType: Cell type annotation<br>LARRY: Error corrected LARRY barcode<br>percent.mt: percentage of mitochondrial DNA<br>nCount_RNA: Read count for the RNA modality<br>nFeature_RNA: Number of RNAs with at least one read<br>nCount_AB: Read count for the surface protein modality<br>nFeature_AB: Number of ABs with at least one read