Additional file 1 of Single-cell genomics identifies distinct B1 cell developmental pathways and reveals aging-related changes in the B-cell receptor repertoire
Creators: name: Luo, Yao
name: Wang, Jing
name: Li, Kairui
name: Li, Mingxia
name: Xu, Shasha
name: Liu, Xingjie
name: Zhang, Zhiwei
name: Xu, Xiang
name: Zhang, Yu
name: Pan, Jiawei
name: Liu, Pengtao
name: Gao, Shaorong
name: Miao, Zhichao
name: Yu, Yong
Publisher: name: figshare
Year: 2022
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1: Figure S1. a The violin plots showing the number of genes, the number of counts and the percentage of mitochondrial genes in all examined samples. b The violin plot showing the percentage of mitochondrial genes in each sample. c The scatter plot showing that the logarithm of the number of genes and the logarithm of the number of counts are linearly correlated. d UMAP plots showing the distribution of the six samples, the number of counts, the number of genes, and the percentage of mitochondrial genes. e The UMAP plots showing the distribution of the re-clustered samples after quality control. f The UMAP plots showing the marker gene expression in macrophages (Cd68, S100a8), T cells (Cd3d, Cd3e), erythrocytes (Hbb-bs, Hba-a1) in all examined samples. The color key indicates the expression level. g The UMAP plots showing the expression of the known B cell marker genes. The color key indicates the expression level. Figure S2. a The bar plot showing the percentages of day 5 and 6 neonate samples in each of the C1-C9 clusters. b The expression patterns of the MHCII molecules related genes and CD138 encoding gene in UMAP plot. The color key indicates the expression level. c Projection of the B2 cell progenitor signature (B2 cell progenitor signature was from a previous study, see more details in Methods). The color key indicates the average log normalized expression of the B1 signature genes over the randomly sampled reference genes. d The dot plot demonstrates cluster-specific gene expression in C1, C2, and C4 cells. e, f The expression pattern of the indicated genes in UMAP plot. The color key indicates the expression level. g FACS plots showing C1-C4 cells were present in neonate peritoneal cavity. Neonates (day 5–6, pool of 12 pups from 1 litter, n = 3) were used for analysis. h FACS plots showing the gating strategy of neonate peritoneal Lin−CD19−C-kitlowSca-1low cells. Neonates (day 6, pool of 12 pups from 2 litters, n = 3) were used. Lineage markers: CD3ε, CD4, CD8α, NK-1.1, Nkp46, CD11b, CD11c, Gr1, Ter119. Data are representative of three (g, h) independent experiments. Figure S3. a The C5-C9 cells are highlighted in the UMAP projection. b, c Distribution of the indicated gene expression in UMAP plots. The color key indicates the expression level. d Table shows the identification markers for B cell subsets (C1-C9) in neonate peritoneal cavity. Figure S4. a The proportion of B1-C5 cluster in B1 cells in each mouse sample. b Bar plot showing the pathway analysis of DEGs that up-regulated (log fold change &gt; 0.1, FDR &lt; 0.01, n = 1, 468 genes) in the B1-C5 cells comparing to B1-C3 cells. The top 10 pathways are presenting. The gene set analysis tool GeneAnalytics (LifeMap Sciences) was used for DEGs pathway analysis. c Distribution of the aging-related gene expression in UMAP plots. The color key indicates the expression level. Figure S5. a The table lists the usages of VH and VL genes of both B1 and B2 cells from differently aged mice. b Bar plot shows the percentages of B1 cell clones that recognize the phosphatidylcholine (both Ighv12-3/Igkv4-91 and Ighv11-2/Igkv14-126 pairings) in examined mature B1 cells from mice of different age. c The expression pattern of the proliferation-related genes in the re-projected mature B1 cell UMAP plot. The color key indicates the expression level. d Bar plot shows percentages and numbers of the B1 cell clones that recognize the phosphatidylcholine (PtC) in mature proliferating B1 subset (B1-C4) in mice of different age.