Additional file 1 of Single-cell RNA sequencing reveals a landscape and targeted treatment of ferroptosis in retinal ischemia/reperfusion injury
Creators: name: Li, Yangyang
name: Wen, Yuwen
name: Liu, Xiuxing
name: Li, Zhuang
name: Lin, Bingying
name: Deng, Caibin
name: Yu, Ziyu
name: Zhu, Yingting
name: Zhao, Ling
name: Su, Wenru
name: Zhuo, Yehong
Publisher: name: figshare
Year: 2022
Subjects: subject: Biochemistry
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
subject: Neuroscience
subject: Physiology
subject: Immunology
subject: FOS: Clinical medicine
subject: Developmental Biology
subject: Hematology

description: Additional file 1: Fig. S1. I/R induced altered heterogeneity in retinal cell constitution. A t-SNE distribution showing a group of myeloid cells with high expression of Itgam and Lyz2, as well as cell subsets with high expression of C1qa and Ly6c2. B Pie plot showing the relative ratio of 12 clusters between Blank (left) and I/R (right) groups. C Violin plots showing the proportion of 4 clusters in retinal cells between Blank and I/R groups (n = 3/group). P value were calculated using a Wilcoxon rank-sum test. D t-SNE distribution shows strategies for CONE clustering and subclassification from retinal cells. E t-SNE distribution shows strategies for ROD clustering and subclassification from retinal cells. F Violin plots showing the proportion of 3 ROD-subclusters between Blank and I/R groups (n = 3/group). P value were calculated using a Wilcoxon rank-sum test. G Inflammation-related GO and pathway enrichment analysis of the CONE-SCs clustering DEGs. P value was derived by a hypergeometric test. H Inflammation-related GO and pathway enrichment analysis of the CONE-SCs clustering DEGs. P value was derived by a hypergeometric test. Fig. S2. I/R induced an expansion of macroglia subclusters with ferroptosis. A t-SNE distribution showing 7 subclusters in macroglia. B t-SNE distribution showing groups (Blank and I/R) in macroglia. C Bar plots showing cell abundances across Mag-SCs (n = 7) for the Blank and I/R groups. D Violin plots showing the proportion of Mag-SC0 in CONE between Blank and I/R groups (n = 3/group). P value were calculated using a Wilcoxon rank-sum test. E Violin plots showing the proportion of 3 Mag-SCs in CONE between Blank and I/R groups (n = 3/group). P value were calculated using a Wilcoxon rank-sum test. F A heat map representing the scaled expression values of the top 10 genes defining each Mag-SCs. G Violin plots showing the expression of gliocyte-related genes in Mag-SCs. H GO and pathway enrichment analysis of the Mag-SCs clustering DEGs. P value was derived by a hypergeometric test. Fig. S3. I/R injury induced an expansion of Myeloid subclusters with ferroptosis and inflammation activation. A Volcano plot showing DEGs that are I/R-upregulated (red) or downregulated (blue) in Myeloid. P value were calculated using a Wilcoxon rank-sum test. B t-SNE distribution shows strategies for Myeloid clustering and subclassification from retinal cells. C Violin plots showing the inflammatory response score (left) and ferroptosis scores (right) between Blank and I/R groups among microglia cluster. D Violin plots showing the expression of genes related to IGF signaling between Blank and I/R groups. E Violin plots showing the expression of genes related to NT signaling between Blank and I/R groups. F Heatmap shows the role and importance of each cluster in SEMA3 signaling network (up). Bar plots showing the relative contribution of each ligand–receptor pair in SEMA3 signaling pathway (down). G Circle plot showing the inferred TNF signaling networks between Blank and I/R groups. H Bar plots showing the relative contribution of each ligand–receptor pair in CCL signaling pathway. I Violin plots showing the expression of genes related to CCL signaling between Blank and I/R groups. J Immunofluorescence image labeling activated macroglia with GFAP(red) is shown. Cell nucleuses were stained with DAPI (blue) (scale bar = 50 μm). K The cell viability showing the cytotoxicity of Fer-1 on primary microglia. Fig. S4. Sorting strategy for CD11B+ microglia in vitro. A Flow cytometry histogram showing the sorting strategy for CD11B+ microglia. B Percentage showing the purification of primary microglia.