Project description:Single cell RNA-seq was used to identify the gene expression signatures and transcript isoforms that distinguish quiescent and activated muscle stem cells in mouse.
Project description:The purpose of this single cell experiment is to compare and characterize at molecular level actively cycling stem cells in the isthmus and quiescent stem cells in the base of the mouse stomach corpus. The lineage tracing data from Stmn1-CreERT2 shows that Stmn1+ cells in the corpus isthmus include fast dividing isthmus stem cells with long-term potency. On the other hand, chief cells including Lgr5+ subpopulation can play as quiescent stem cells in the base that are largely quiescent in homeostasis, but are activated upon injury. The isthmus stem cells and chief cells are isolated by Stmn1 and Pgc, respectively, and were subject to single cell RNA-seq experiment.
Project description:The study of gene expression in mammalian single cells using genomic technologies now provides the possibility to investigate the patterns of allelic gene expression. We have used single-cell RNA sequencing to detect the allele-specific mRNA level in 203 single human primary fibroblast cells over 133,633 unique heterozygous single nucleotide variants (hetSNVs). We have observed that at the snapshot of analyses each cell contains mostly transcripts from one allele from the majority of genes; indeed 76.4% of the hetSNVs display stochastic monoallelic expression in single cells. Remarkably, adjacent hetSNVs exhibit haplotype consistent allelic ratio; in contrast distant sites located in two different genes are independent of the haplotype structure. Moreover, the allele-specific expression in single cells correlated with the abundance of the cellular transcript. We observed that genes expressing both alleles in majority of the single cells at a given time point are rare and enriched in highly expressed genes. The relative abundance of each allele in a cell is controlled by some regulatory mechanisms since we observed related single-cell allelic profiles according to genes. Overall, these results have direct implications in cellular phenotypic variability.
Project description:Through single cell transcriptome analysis, we uncovered molecular signatures of CD133+/GFAP- ependymal (E) cells, CD133+/GFAP+ neural stem (B) cells, Dlx2+ neuroblasts (A cells), and Sox10+ oligodendrocyte progenitors (O cells) in the adult mouse forebrain neurogenic zone. prominent hub genes of the gene network unique to ependymal CD133+/GFAP- quiescent cells are enriched for receptors of angiogenic factors and immune-responsive genes. Administration of VEGF activated CD133+ ependymal stem cells lining not only the lateral, but also the 4th ventricles, and together with bFGF, elicited subsequent neural lineage differentiation and migration. Examination of 28 single cells and 4 populations of 10 cells from adult mouse forebrain neurogenic zone.
Project description:Quiescent stem cells of glioblastoma (GBM), a malignant primary brain tumor, are potential sources for recurrence after therapy. However, the gene expression program underlying the physiology of GBM stem cells remains unclear. We have isolated quiescent GBM cells by engineering them with a knock-in H2B-GFP proliferation reporter and expanding them in a 3D tumor organoid model that mimics tumor heterogeneity. H2B-GFP label retaining quiescent cells were subjected to stem cell assays and RNA-Seq gene expression analysis. While quiescent GBM cells were similar in clonal culture assays to their proliferative counterparts, they displayed higher therapy resistance. Interestingly, quiescent GBM cells upregulated epithelial-mesenchymal transition (EMT) genes and genes of extracellular matrix components. Our findings connect quiescent GBM cells with an EMT-like shift, possibly explaining how GBM stem cells achieve high therapy resistance and invasiveness, and suggest new targets to abrogate GBM.
Project description:In order to identify the transcriptome change and heterogeneity in replicative senescent cells and stress-induced senescent cells, =we measured 1600 single cell transcriptomes of young quiescent cells at a population doubling (PD) number of 38, middle age quiescent cells (PD = 48), replicative senescent (PD = 71) cells and 50Gy X-ray induced senescent cells of PD38 control cells by Drop-seq.
Project description:Follicular Lymphomas are blood tumors growing as spheres in patients. Before this study, there was no experimental model mimicking the 3D organization of these in vivo tumors. We develop such a model, called MALC, and observed a progressive enrichment in quiescent cells in these with time of culture; these cells were sorted, as their cycling counterparts, and their transcriptomes were compared. We used microarrays to detail the differential global gene expression profile between quiescent and cycling cells isolated from MALC.
