Additional file 1 of Keratinocytes drive the epithelial hyperplasia key to sea lice resistance in coho salmon
Creators: name: Salisbury, S. J.
name: Daniels, R. Ruiz
name: Monaghan, S. J.
name: Bron, J. E.
name: Villamayor, P. R.
name: Gervais, O.
name: Fast, M. D.
name: Sveen, L.
name: Houston, R. D.
name: Robinson, N.
name: Robledo, D.
Publisher: name: figshare
Year: 2024
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1: Figs. S1–S55 and Tables S1–S9. Figs. S1–S55: Fig. S1 Expression of marker genes within 23 identified cell clusters within Atlantic salmon fin and skin samples. Fig. S2 Expression of marker genes within 23 identified cell clusters within coho salmon fin and skin samples. Fig. S3 Violin plots of the expression of marker genes from Fig. 1c for each cell type detected within Atlantic salmon samples split by tissue type. Fig. S4 Violin plots of the expression of marker genes from Fig. 1d for each cell type detected within coho salmon samples split by tissue type. Fig. S5 Violin plots of expression levels for the top 20 significant marker genes for the mucous (1) cluster of the coho salmon dataset. Fig. S6 Violin plots of expression levels for the top 20 significant marker genes for the mucous (2) cluster of the coho salmon dataset. Fig. S7 Violin plots of expression levels for the top 20 significant marker genes for the undifferentiated cluster of the Atlantic salmon dataset. Fig. S8 Expression of CD45 (ptprc) in Atlantic salmon (a, b) and coho salmon (c, d). Fig. S9 Violin plots of expression levels for the top 20 significant marker genes for the T cells (1) cluster of the Atlantic salmon immune cells only data subset. Fig. S10 Violin plots of expression levels for the top 20 significant marker genes for the T cells (2) cluster of the Atlantic salmon immune cells only data subset. Fig. S11 Violin plots of expression levels for the top 20 significant marker genes for the T cells (3) cluster of the Atlantic salmon immune cells only data subset. Fig. S12 Violin plots of expression levels for the top 20 significant marker genes for the T cells (4) cluster of the Atlantic salmon immune cells only data subset. Fig. S13 Violin plots of expression levels for the top 20 significant marker genes for the T cells (5) cluster of the Atlantic salmon immune cells only data subset. Fig. S14 Violin plots of expression levels for the top 20 significant marker genes for B cells of the Atlantic salmon immune cells only data subset. Fig. S15 Violin plots of expression levels for the top 20 significant marker genes for dendritic cells of the Atlantic salmon immune cells only data subset. Fig. S16 Violin plots of expression levels for the top 20 significant marker genes for neutrophils of the Atlantic salmon immune cells only data subset. Fig. S17 Violin plots of expression levels for the top 20 significant marker genes for the macrophages (1) cluster of the Atlantic salmon immune cells only data subset. Fig. S18 Violin plots of expression levels for the top 20 significant marker genes for the macrophages (2) cluster of the Atlantic salmon immune cells only data subset. Fig. S19 Violin plots of expression levels for the top 20 significant marker genes for the macrophages (3) cluster of the Atlantic salmon immune cells only data subset. Fig. S20 Violin plots of expression levels for the top 20 significant marker genes for monocytes of the Atlantic salmon immune cells only data subset. Fig. S21 Violin plots of expression levels for the top 20 significant marker genes for the T cells (1) cluster of the coho salmon immune cells only data subset. Fig. S22 Violin plots of expression levels for the top 20 significant marker genes for the T cells (2) cluster of the coho salmon immune cells only data subset. Fig. S23 Violin plots of expression levels for the top 20 significant marker genes for the T cells (3) cluster of the coho salmon immune cells only data subset. Fig. S24 Violin plots of expression levels for the top 20 significant marker genes for the T cells (4) cluster of the coho salmon immune cells only data subset. Fig. S25 Violin plots of expression levels for the top 20 significant marker genes for the T cells (5) cluster of the coho salmon immune cells only data subset. Fig. S26 Violin plots of expression levels for the top 20 significant marker genes for B cells of the coho salmon immune cells only data subset. Fig. S27 Violin plots of expression levels for the top 20 significant marker genes for dendritic cells of the coho salmon immune cells only data subset. Fig. S28 Violin plots of expression levels for the top 20 significant marker genes for neutrophils of the coho salmon immune cells only data subset. Fig. S29 Violin plots of expression levels for the top 20 significant marker genes for the macrophages (1) cluster of the coho salmon immune cells only data subset. Fig. S30 Violin plots of expression levels for the top 20 significant marker genes for the macrophages (2) cluster of the coho salmon immune cells only data subset. Fig. S31 Violin plots of expression levels for the top 20 significant marker genes for monocytes of the coho salmon immune cells only data subset. Fig. S32 Expression of CD4 and CD8 paralogs in the immune cell subclusters identified within a) Atlantic salmon and b) coho salmon. Fig. S33 Number of genes detected as differentially expressed between the control samples and each of the infected time points for each cell type for a) Atlantic salmon and b) coho salmon. Fig. S34 Number of times each gene was detected as differentially expressed (1–5 time points) between any of the treatment time points and the control sample for a given cell type detected within the Atlantic salmon samples. Fig. S35 Number of times each gene was detected as differentially expressed (1–5 time points) between any of the treatment time points and the control sample for a given cell type detected within the coho salmon samples. Fig. S36 Significantly enriched biological GO terms for each Atlantic salmon cell type based on the significantly differentially expressed genes detected between the control samples and any of the five treatment time points. Fig. S37 Significantly enriched biological GO terms for each coho salmon cell type based on the significantly differentially expressed genes detected between the control samples and any of the five treatment time points. Fig. S38 Summary statistics for all Atlantic and coho salmon libraries. Fig. S39 Percent of UMIs identified as mtDNA features for a) Atlantic salmon and b) coho salmon samples, with the 10% maximum threshold used for subsequent filtering indicated by a horizontal black line. Fig. S40 UMI and feature counts per cell barcode and feature counts vs. UMI counts for each Atlantic salmon sample. Fig. S41 UMI and feature counts per cell barcode and feature counts vs. UMI counts for each coho salmon sample. Fig. S42 Cell clusters after initial integration of Atlantic salmon samples: a) UMAP, b) number of cells per cluster per sample, c) violin plot of the distribution of feature counts per cluster, d) violin plot of the distribution of UMI counts per cluster. Fig. S43 Cell clusters after initial integration of coho salmon samples: a) UMAP, b) number of cells per cluster per sample, c) violin plot of the distribution of feature counts per cluster, d) violin plot of the distribution of UMI counts per cluster. Fig. S44 Violin plots of expression levels for the top 20 significant marker genes for cluster 0 after the initial integration of Atlantic salmon samples. Fig. S45 Violin plots of expression levels for the top 20 significant marker genes for cluster 1 after the initial integration of coho salmon samples. Fig. S46 Cell clusters after removing one cluster (cluster 1 from Fig. S43) and re-integrating/clustering coho salmon samples: a) UMAP, b) number of cells per cluster per sample, c) violin plot of the distribution of feature counts per cluster, d) violin plot of the distribution of UMI counts per cluster. Fig. S47 Violin plots of expression levels for the top 20 significant marker genes for cluster 11 after removing one cluster (cluster 1 from Fig. S43) and re-integrating/clustering coho salmon samples. Fig. S48 Distribution of UMIs and features for Atlantic salmon (a, b) and coho salmon (c, d) samples. Fig. S49 Subclustering of cluster 12 within coho salmon. Feature plots indicate expression of ltk (a) and casq1b (b) in different cells within cluster 12. Reclustering those cells within cluster 12 using 3 PCs and a resolution of 0.02 revealed two clusters as visualized in a UMAP (c). One cluster expressed casq1b, the other expressed ltk as shown in a dot plot (d) and feature plots (e, f). Fig. S50 Distribution of UMIs and features for each cluster identified in Atlantic salmon (a, b) and coho salmon (c, d). Fig. S51 Cell clusters after initial integration of Atlantic and coho salmon samples: a) UMAP, b) number of cells per cluster per sample, c) violin plot of the distribution of feature counts per cluster, d) violin plot of the distribution of UMI counts per cluster. Fig. S52 Violin plots of expression levels for the 9 significant marker genes for cluster 0 of the dataset integrating both Atlantic salmon and coho salmon samples. Fig. S53 Cell clusters after removing one cluster (cluster 0 from Fig. S51) and re-integrating/clustering: a) UMAP, b) number of cells per cluster per sample, c) violin plot of the distribution of feature counts per cluster, d) violin plot of the distribution of UMI counts per cluster. Fig. S54 Violin plots of expression levels for the 7 significant marker genes for cluster 1 of the dataset integrating both Atlantic and coho samples (for UMAP see Fig. S53). Fig. S55 Cell clusters after removing one cluster (cluster 1 from Fig. S53) and re-integrating/clustering: a) violin plot of the distribution of feature counts per cluster, b) violin plot of the distribution of UMI counts per cluster, c) number of cells per cluster per sample. Tables S1–S9: Table S1 Summary statistics for STAR outputs for each Atlantic salmon sample. Table S2 Summary statistics for STAR outputs for each coho salmon sample. Table S3 Number of nuclei detected per sample after several filtering stages. Table S4 Number of cells per cell type in each Atlantic salmon sample. Table S5 Number of cells per cell type in each coho salmon sample. Table S6 Number of cells per cluster and sampling time point after reclustering only the immune cells within the Atlantic salmon samples. Table S7 Number of cells per cluster after reclustering only the immune cells within the coho salmon samples. Table S8 Genes used for cell cycle scoring for Atlantic salmon. Table S9 Genes used for cell cycle scoring for coho salmon.