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