Additional file 2 of Single-cell analysis of a salmonid immune system (river brown trout Salmo trutta fario) reveals evolutionary divergence and hatchery-induced transcriptional reprogramming

Additional file 2. Table S1 List of genes used as “prior markers” for putative cell type assignments of clusters and associated notes. Table S2 List of marker genes for all clusters as identified using the FindAllMarkers() function in Seurat. Additional information includes gene names and descriptions and whether the gene is a “prior marker.” Table S3 Compiled output from GO term enrichment of high-abundance markers (pct.1 >/= 0.6 and log2FC >/= 1) for each of 23 clusters. Tables S4–S7 Genes found to be markers exclusively of neutrophil (Table S4), macrophage (Table S5), T-cell (Table S6), and B-cell clusters (Table S7), respectively, i.e., genes that were markers of that specific putative cell type and not markers of other putative cell types. Clusters of which the gene is a high-abundance marker (pct.1 >/= 0.6) and those of which the gene is a marker regardless of abundance are listed in columns 2 and 7, respectively. In Table S7, an additional column denotes whether the gene encodes a putative immunoglobulin. Table S8 Categorization of 175 ohnologue pairs among variably expressed genes according to differences in or similarity of expression patterns across clusters. Pairs are labeled according to the gene ID of the corresponding Esox lucius homologue. Tables S9–S12 Genes differentially expressed in pseudobulk in clusters M1 (Table S9), N1 (Table S10), B3 (Table S11), and T5 (Table S12) in fish of “mix” or “farm” origin relative to “wild” origin. Table S13 Enriched GO terms (molecular function) among genes differentially expressed in pseudobulk in “mix” or “farm” origin fish relative to “wild”.