EPI-Clone dataset X.1 : Targeted DNAm+DNA+RNA-seq from CD34+ BM cells of a healthy donor

This is dataset supports parts of the EPI-Clone manuscript. Here, targeted single cell methylation profiling (scTAMseq) was combined with targeted RNA-seq from the same cells (SDR-seq) to profile CD34+ cells from bone marrow of a healthy 51-year old male individual.Dataset is a seurat (v5) object with the following assays, reductions and metadata:<br><b>ASSAYS:</b><br>RNA: RNA expression data for 120 target genesDNAm: 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 scTAMseq<b>DIMENSIONALITY REDUCTION</b>pca, dynapca: PCA performed on all methylome data, or on consensus dynamic CpGs onlyumap, dynaumap: UMAP computed on all methylome data, or on consensus dynamic CpGs onlyprojected: Methylome data projected on the reference CD34+ UMAP coordinate (add DOI!)rnapca: PCA performed on RNA datarnaumap: PCA performed on RNA dataFor strategies how to obtain dimensionality reduction that reflect clonal identity, please see the github page accompanying the manuscript.<b>METADATA</b>nFeature_RNA, nFeature_DNAm, nFeature_NonHhaI: Number of RNA , DNAm and genotypoing amplicons observedprojected.cluster: Cell type, according to DNA methylation based projection on the CD34+ referenceCellType_rna: Cell type annotation according to RNA expressionCountsChrY: Y chromosome read countsEPIclone_id: Clone, according to EPI-clone algorithm