Expression of the Autoimmune regulator (AIRE) outside of the thymus has long been suggested in both humans and mice, but the cellular source in humans has remained undefined. Here we identify AIRE expression in human tonsils and extensively analyzed these "extra-thymic AIRE expressing cells" (eTACs) using combinations of flow cytometry, CyTOF and single cell RNA-sequencing. We identified AIRE+ cells as dendritic cells (DCs) with a mature and migratory phenotype including high levels of antigen p ...[more]
Project description:Differentiation into diverse cell lineages requires orchestration of gene regulatory networks guiding cell fate choices. Genetic factors acting through changes in transcriptional levels can contribute to cardiovascular disease risk by impacting early stages of development and have cell type-specific effects. We set out to characterize lineage trajectory progression of subpopulations and identify potential disease-related genes by examining their expression changes in single cells during early stages of cardiac lineage specification. Using 43,168 single-cell transcriptomes, we developed novel classification and trajectory analysis methods to dissect cellular composition and gene networks across five discrete time points underlying lineage derivation of mesoderm, definitive endoderm, vascular endothelium, cardiac precursors, and definitive cell types that comprise cardiomyocytes and a previously unrecognized cardiac outflow tract population.
Project description:Gastrulation represents a pivotal point in mammalian development, when the basic body plan is established and cells are specified into one of the three germ layers. This is followed by rapid diversification into specific lineages and the appearance of the various cell types required to build each of the organs. The rich variety of cell types present at this stage has never been rigorously characterised in any mammalian organism, and thus insight into cell fate decisions and the underlying regulatory networks have been inaccessible. We have used droplet based single-cell RNA-sequencing to address this by profiling ~7000 cells from three E8.25 mouse embryos.
Project description:Gastrulation represents a pivotal point in mammalian development, when the basic body plan is established and cells are specified into one of the three germ layers. This is followed by rapid diversification into specific lineages and the appearance of the various cell types required to build each of the organs. The rich variety of cell types present at this stage has never been rigorously characterised in any mammalian organism, and thus insight into cell fate decisions and the underlying regulatory networks have been inaccessible. We have used droplet based single-cell RNA-sequencing to address this by profiling ~20000 cells from C57BL/6 E8.25 mouse embryos.
Project description:We performed 3' single-cell RNA-seq using the 10X Genomics Chromium (version 1 chemistry) system on ~19,000 undifferentiated human IPSCs to explore the cellular heterogeneity of a seemingly homogeneous cell population.
Project description:Mice intranasally exposed to a low dose of LPS (i.e., 100 ng) are prone to develop features of allergic asthma upon subsequent exposure to house dust mites (HDM) allergens, while mice exposed to vehicle or 100 µg LPS do not develop such features. In order to understand the mechanisms that promote allergic asthma, we sought to characterize the lung neutrophils, which are massively recruited after LPS exposure, by single cell RNA-Seq.
Project description:Population control for the scRNA-seq based analysis a well-established fraction of mouse subcutaneous adipose-derived stromal vascular fraction (SVF) cells that is generally considered to harbour adipogenic stem and progenitor cells (ASPCs). We collected Lin- (CD31- CD45- TER119-) CD29+ CD34+ SCA1+ cells from the mouse subcutaneous SVF of transgenic mice, in which red fluorescent protein (RFP) is induced in Dlk1-expressing cells upon feeding with tamoxifen. While CD29, CD34, and SCA1 are generally expected to enrich for stem cells, DLK1 has previously been suggested to specifically mark pre-adipocytes.
Project description:Xist orchestrates X chromosome inactivation, a process that entails chromosome-wide silencing and remodeling of the 3-dimensional structure of the X chromosome. Yet, it remains unclear whether these changes in nuclear structure are mediated by Xist and whether they are required for silencing. Here we show that Xist directly interacts with the Lamin B Receptor (LBR), an integral component of the nuclear lamina, and that this interaction is required for Xist-mediated silencing. We show that this interaction recruits the inactive X to the nuclear lamina and by doing so enables Xist to spread to actively transcribed genes across the X. Our results demonstrate that lamina recruitment changes the accessibility of DNA thereby enabling Xist, and its silencing proteins, to spread across the X to silence transcription. We examined the genomic localization of the Xist lncRNA using RNA Antisense Purification (RAP) in male mouse ES cells where the endogenous Xist promoter is replaced by a tet-inducible one (pSM33) containing 1) wild-type Xist (WT), 2) A-repeat deletion Xist (dA), 3) LBR binding site deletion Xist (dLBS), 4) dLBS-Xist rescued with LMNB1 (LMNB1Res), 5) LBR CRISPRi knock down (LBRKD), or 6) SHARP CRISPRi knock down (SHARPKD).
Project description:We used the resolving power of single-cell transcriptional profiling to molecularly characterize the mouse adipose stem and progenitor cell-enriched, subcutaneous adipose stromal vascular fraction. We molecularly assessed CD45- CD31- SVF cells using the 10x Genomics Chromium (10x) platform.
Project description:We sought to evaluate in an unbiased way the heterogeneity of lung interstitial macrophages and their relationship with alveolar macrophages, lung Ly-6Chi classical monocytes and Ly-6Clo patrolling monocytes, by single cell RNA-Seq.
Project description:Endothelial cells are generated independently in the yolk sac, allantois and embryo proper. We dissected embryos from embryonic day 8.25 and captured individual cells from each of these positions within the embryo to investigate how their transcriptional signatures differ. Single-cell libraries were prepared for sequencing using the Smart-seq2 protocol.