Project description:Macrophages play an important role in the pathological process of stroke. We used single cell RNA sequencing (scRNA-seq) to analyze the diversity of infiltrated macrophages from ischemic brain after stroke.
Project description:Neurogenesis after stroke compounded with amyloid beta plaques around the cerebral vasculature has implications in delaying tissue recovery. We used single cell RNA sequencing (scRNA-seq) to understand the cellular interactions in the hippocampus during post-stroke recovery with CAA.
Project description:Microglia are resident myeloid cells in the central nervous system (CNS) that regulate homeostasis and protect CNS from damage and infection. The phenotype of microglia is critical in regulating the propagation and resolution of inflammatory responses after ischemic stroke. However, little is known of its complexity and heterogeneity in the above context. Here, using single-cell RNA sequencing (scRNA-seq) of over 11,000 cells from the mice ischemic brain tissues, we demonstrated a previously undefined molecular heterogeneity among microglia clusters following ischemic stroke.
Project description:The momentum of scRNA-seq datasets prompts for simple and powerful tools exploring their meaningful signatures. Here we present Single-Cell_Signature_Explorer (https://sites.google.com/site/fredsoftwares/products/single-cell-signature-explorer), the first method for qualitative and high-throughput scoring of any gene set-based signature at the single cell level and its visualization using t-SNE or UMAP. By scanning datasets for single or combined signatures, it rapidly maps any multi-gene feature, exemplified here with signatures of cell lineages, biological hallmarks and metabolic pathways in large scRNAseq datasets of human PBMC, melanoma, lung cancer and adult testis.
Project description:Neurons showed both spatial and temporal distinctions while glial cells were much uniform among the regions. We captured the developmental course of oligodendrocytes and found human specific cell state comparing to that in mouse. A new subcluster of NPCs were identified in particular embryonic weeks from GW11 to GW14, which destinated to deeper layers. We specified the progress of human deeper layer, upper layer and mature neuron genesis along the time and their intrinsic regulations. Regional characters was revealed both for cortical regions and the pons. With the systematic single cell analysis, we uncovered human embryonic neural development on both temporal and spatial scale, which offered deeper insights into the human neurogenesis and cortical development.
Project description:Here, we used single cell RNA-sequencing (scRNA-seq) to profile pluripotent stem cell derived human intestinal organoids (HIOs) grown in matrigel or a non-adhesive alginate hydrogel after 28 days of in vitro growth. Additionally, we used scRNA-seq to profile HIOs derived in the presence of Neuregulin 1 (NRG1) and/or EGF after 40 days of in vitro growth.