(A) Representative images of unsorted BAT adipocytes from untreated or CL 316,243-treated WT or UCP1-KO mice stained with isotype control or anti-UCP1 antibody (red). Intact cells are co-stained with Syto-12 (green). Note the complete lack of UCP1 staining in the knockout sample. Scale bars, 50 μm.
a Overview of the ligand-receptor interaction database. CellChatDB takes into account known composition of the ligand-receptor complexes, including complexes with multimeric ligands and receptors, as well as several cofactor types: soluble agonists, antagonists, co-stimulatory and co-inhibitory membrane-bound receptors. CellChatDB contains 2021 validated interactions, including 60% of secreting interactions. In addition, 48% of the interactions involve heteromeric molecular complexes. b CellChat either requires user assigned cell labels as input or automatically groups cells based on the low-dimensional data representation supplied as input. c CellChat models the communication probability and identifies significant communications. d CellChat offers several visualization outputs for different analytical tasks. Different colors in the hierarchy plot and circle plot represent different cell groups. Colors in the bubble plot are proportional to the communication probability, where dark and yellow colors correspond to the smallest and largest values. e CellChat quantitatively measures networks through approaches from graph theory, pattern recognition and manifold learning, to better facilitate the interpretation of intercellular communication networks and the identification of design principles. In addition to analyzing individual dataset, CellChat also delineates signaling changes across different contexts, such as different developmental stages and biological conditions.
LS Models Unsorted Pictures
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Mouse skin wound dataset. We used our recently published scRNA-seq dataset from mouse skin wounds23. This dataset included 21,819 cells and was generated via 10X Genomics platform (GEO accession code: GSE113854). Briefly, scRNA-seq was performed on unsorted cells isolated from mouse skin wound dermis from day 12 post-wounding. Unsupervised clustering identified fibroblasts (FIB, 65%), immune cell populations, including myeloid cells (MYL, 15%), T lymphocytes (TCELL, 4%), B lymphocytes (BCELL, 3%), dendritic cells (DC, 1%), endothelial cells (ENDO, 9%), lymphatic endothelial cells (LYME, 1%), Schwann cells (SCH, 1%) and red blood cells (RBC, 1%). For the intercellular communication analysis, we excluded red blood cells and used the remaining 21,557 cells. The digital data matrices were normalized by a global method, in which the expression value of each gene was divided by the total expression in each cell and multiplied by a scale factor (10,000 by default). These values were then log-transformed with a pseudocount of 1. Normalized data were used for all the analyses. To investigate the heterogeneity of intercellular communications among different cell subpopulations, we performed subclustering analysis on the cell types, whose abundance in the dataset was greater than 5% using the Louvain community detection method. The number of cell groups was determined by the eigengap approach. 2ff7e9595c
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