Additional file 1 of Single-cell RNA sequencing reveals roles of unique retinal microglia types in early diabetic retinopathy
Creators: name: Wang, Yan
name: Yang, Xiongyi
name: Zhang, Yuxi
name: Hong, Libing
name: Xie, Zhuohang
name: Jiang, Wenmin
name: Chen, Lin
name: Xiong, Ke
name: Yang, Siyu
name: Lin, Meiping
name: Guo, Xi
name: Li, Qiumo
name: Deng, Xiaoqing
name: Lin, Yanhui
name: Cao, Mingzhe
name: Yi, Guoguo
name: Fu, Min
Publisher: name: figshare
Year: 2024
Subjects: subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Neuroscience
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer
subject: Virology

description: Additional file 1: Figure S1. (A) The figure shows the number of high-quality cells retained for each sample after quality control. (B) UMAP plot shows 33 clusters (Red Blood Cells excluded). (C) Featureplot shows the classic marker genes of each cell type. Color scale: red, high expression; gray, low expression. (D) Pie graph and histogram show the number of each cell type. (E) Bar plot shows the number of each cell type in different stages of DR. (F) Gene-expression heatmap of the top marker genes for each cell type. Color scale: red, high expression; gray, low expression. Figure S2. (A) Histogram shows the GO analysis results of Rods. Color and length indicate the adjust p-values of each pathway. (B) Featureplot shows the expression of Opn1mw and Opn1sw in Cones. Color scale: red and oringe, high expression; gray, low expression. (C) Venn plot shows the number of cells expressing Opn1mw and Opn1sw genes in Cones. The intersection area represents the number of Opn1mw + Opn1sw + cells, and the blank area represents the number of Opn1mw-Opn1sw- cells. (D) Violin plot shows the expression of marker genes in five BC subgroups. (E) Bubble plot shows the markers of AC and AC/HC. The size of each circle is proportional to the percentage of cells expressing the gene. The color of each circle represents the level of gene expression in the cell. (F) Ridge plot shows the expression of marker genes in AC/HC. Onecut1 is the marker for HC. Slc6a9 and Gjd2 are markers for AC. (G) Ridge plots shows the expression of markers of microglia (C1qa, Aif1, Apoe, Tmem119), blood derived macrophages (Cxcr4, Cd53, Ptprc) and perivascular macrophages (Cd163, Mrc1) in macrophages. (H) The outgoing and incoming communication pathways associated with inflammation in non-neuronal cells. Color scale: green, high relative strength; white, low relative strength. Figure S3. (A) UMAP plot of three subtypes of microglia (left) and a magnified version (right). (B) Heatmap shows the highly expressed genes of three subtypes of microglia. Color scale: red, high expression; gray, low expression. (C) Featureplot shows the expression of marker genes in microglia. C1qa is used to identify microglia, Tmem119 and Ccr5 are used to distinguish M1 and M2, and Egr2 is used to distinguish two subgroups of M1. (D) Immunofluorescent labelling for C1qa(red), Ccr5(green), and DAPI nuclear staining (blue) in the rat retina. M1 is indicated by arrows and M2 is indicated by arrowheads (first row, 20X). Immunofluorescent labelling for Ccr5(red), Egr2(green), and DAPI nuclear staining (blue) in the rat retina. Egr2 + M1 is indicated by arrows and Egr2-M1 is indicated by arrowheads (second row, 20X). Scale bar 50 um. (E) Immunofluorescent labelling for C1qa(red), Ccr5(green), and DAPI nuclear staining (blue) in the rat retina. M1 is indicated by arrows and M2 is indicated by arrowheads (left, 20X; first row, 40X). Immunofluorescent labelling for Ccr5(red), Egr2-(green), and DAPI nuclear staining (blue) in the rat retina. Egr2 + M1 is indicated by arrows and Egr2-M1 is indicated by arrowheads (second row, 40X). Scale bar 50 um(left); 20um(right). (F) Immunofluorescent labelling for C1qa(red), Ccr5(green), and DAPI nuclear staining (blue) in the rat retina. M1 is indicated by arrows and M2 is indicated by arrowheads (63X). Scale bar 20 um. Figure S4. (A) Pseudotime trajectory analysis shows the polarization characteristics of three groups of microglia. Different colors represent different microglia subtypes. The arrows point to the start and end points of the trajectory. (B) The histogram shows the PPI analysis results of TOP 30 genes in Module 5, and the length represents the number of nodes. Table S1. Markers of major cell types. Table S2. New markers for each major cell population. Table S3. Blood glucose levels and weight.