Gene expression profile at single cell level of Lin-Sca-1+c-Kit+ cells (LSKs) from miR-142 WT CML mice (CP LSC) and of LSKs from miR-142 KO CML mice (BC LSC). [scRNA-Seq]

To assess how the miR-142 deficit affected the BM LSC-enriched LSK landscape, we conducted a single cell RNA-seq analysis of BM miR-142+/+ BCR-ABL (CP CML) and miR-142−/− BCR-ABL (BC CML) LSKs which were harvested from the respective mice, 2 weeks after BCR-ABL induction. ~8000 cells per sample were captured on a 10x Genomics Chromium using a Next GEM Single Cell 3' GEM kit V3.1 (10xGenomics). Using the Leiden clustering algorithm to identify groups of cells with similar transcriptomes, we identified 8 distinct LSK clusters. We annotated these clusters into distinct lineage-primed subsets using the expression levels of hematopoietic gene transcription factors and cluster differentiation (CD) antigens.