Dataset for the manuscript "Identification of leukemic and pre-leukemic stem cells by clonal tracking from single-cell transcriptomics"

Data accompanying Velten, Story, Hernandez et al., 2021. zip file containing this README and MutaSeq.final.seurat.RDS<br> - a single Seurat (v3.1.4) object containing the following <b>ASSAYS</b>:* RNA: Raw count data (slot: counts), data normalized individually for each patient using default seurat routines (slot: data)* integrated: Scanorama corrected data.<br>* FACS: FACS index values for surface antigens. Logicle transformation was applied where appropriate<br>* counts.mutant.P1: For all mutations analyzed for patient P1, counts of the MUTANT allele. Columns starting with X correspond to mitochondrial sites.* counts.reference.P1: For all mutations analyzed for patient P1, counts of the REFERENCE allele.* PhiSICS.Likelihood.P1: For each cell, likelihood to attach to a given node in the phylogenetic tree (see manuscript figure 2).* PhiSCS.Summarised.P1: Likelihood summarised by main clones (i.e. leukemic.KLF7, leukemic.CEBPA, preleukemic, T.cell.clone, non-leukemic)<br>* counts.mutant.P2: For all mutations analyzed for patient P2, counts of the MUTANT allele. Columns starting with X correspond to mitochondrial sites.* counts.reference.P2: For all mutations analyzed for patient P2, counts of the REFERENCE allele.* PhiSICS.Likelihood.P2: For each cell, likelihood to attach to a given node in the phylogenetic tree (see manuscript figure 2).* PhiSCS.Summarised.P2: Likelihood summarised by main clones (i.e. leukemic, preleukemic, non-leukemic)<br>and the following <b>REDUCTIONS</b>:* scanorama: Scanorama result.* tsne: Computed from scanorama.* umap: Computed from scanorama.<br>and the following <b>METADATA</b> columns:* nCount_RNA: Number of reads mapping to exons.* nFeature_RNA: Number of genes observed.* Plate: Processing plate* patient: Patient* mainClone: Maximum likelihood estimate of the clone the cell belongs to. Also includes estimated clone for P3 and P4, see manuscript figure 4.* Cancer: Boolean variable to distinguish cells that are likely leukemic/preleukemic (TRUE) from other cells (FALSE). Cells with no observations from P3 and P4 are NA.