Code and data for: Distinct tumor genomic signatures underlie canine macrophage polarization

Distinct tumor genomic signatures underlie canine macrophage polarization This dataset accompanies the manuscript "Distinct tumor genomic signatures underlie canine macrophage polarization." It contains cytokine assay data and RNA-sequencing analysis outputs investigating how canine cancer cell line gene expression correlates with macrophage polarization capacity. The dataset includes: (1) raw cytokine concentrations (CCL2, VEGF, TGF-β, TNF-α, IL-8, IL-10, KC-like) from macrophages stimulated with tumor-conditioned media from 25 canine cancer cell lines; (2) Spearman's rank correlation results between tumor transcriptomic features and cytokine secretion; (3) differential gene expression results comparing high- versus low-polarizing cell lines; (4) gene set enrichment analysis (GSEA) outputs; and (5) validation data for two key findings: MVB12A expression associated with VEGF stimulation via exosome-mediated mechanisms, and CCL3 expression associated with TNF-α secretion in histiocytic sarcoma cell lines. Folder structure Files are organized into six folders: raw_cytokines/ — Raw cytokine concentrations from macrophage stimulation experiments spearman_correlations/ — RNA-seq correlation analysis results DEGs/ — Differential gene expression results GSEA/ — Gene set enrichment analysis results CCL3_validation/ — CCL3/TNF-α validation experiment data VEGF_exosome_validation/ — VEGF/exosome validation experiment data Files and variables Raw cytokine data (raw_cytokines/) File: Cytokine_Raw_Values_CCL2.csv Description: Raw CCL2 concentrations (pg/mL) measured by ELISA from macrophages treated with tumor-conditioned media from each cell line (n=3 donors). File: Cytokine_Raw_Values_TGFb.csv Description: Raw TGF-β concentrations (pg/mL) measured by ELISA from macrophages treated with tumor-conditioned media from each cell line (n=3 donors). File: Cytokine_Raw_Values_VEGF.csv Description: Raw VEGF concentrations (pg/mL) measured by ELISA from macrophages treated with tumor-conditioned media from each cell line (n=3 donors). File: Cytokine_Raw_Values_Milliplex.csv Description: Raw cytokine concentrations (pg/mL) measured by 13-plex Milliplex assay (IL-8, IL-10, KC-like, TNF-α, and others) from macrophages treated with tumor-conditioned media (n=3 donors). File: Cytokine_Raw_Values_Ctrl_cells.csv Description: Raw cytokine concentrations (pg/mL) from unstimulated control macrophages (n=3 donors). File: Cytokine_Raw_Values_Cell_counts.csv Description: Number of cancer cells present at time of tumor-conditioned media harvest for each cell line. RNA-sequencing correlation analyses (spearman_correlations/) File: Spearman_correlations_(cytokine)_(normalization).csv Description: Spearman's rank correlation results between gene expression and cytokine modified z-scores. Separate files for each cytokine (CCL2, IL-8, IL-10, KC-like, TGF-β, TNF-α, VEGF) and normalization method (RUVg or TPM). Differential gene expression (DEGs/) File: DEGs_(cytokine).csv Description: Differential gene expression results (DESeq2) comparing high- versus low-polarizing cell lines for each cytokine. High and low groups defined by top and bottom quartiles of modified z-scores (n=6 cell lines per group). Gene set enrichment analysis (GSEA/) File: GSEA_(cytokine).csv Description: Pre-ranked gene set enrichment analysis results for each cytokine using MSigDB Hallmark, Curated (C2), Oncogenic (C6), and Immunologic (C7) collections. CCL3/TNF-α validation (CCL3_validation/) File: CCL3_TNF-a_stimulation.csv Description: TNF-α secretion from macrophages stimulated with recombinant canine CCL3. Variables: donor: Macrophage donor (Dogs 1–4) dose: Recombinant CCL3 concentration (pg/mL) tnfa: TNF-α secreted by macrophages (ng/mL) File: CCL3_CCL3_in_TCM_and_mRNA.csv Description: CCL3 protein levels in tumor-conditioned media (ELISA, pg/mL) and CCL3 mRNA counts (RUVg-normalized) across cell lines. VEGF/exosome validation (VEGF_exosome_validation/) File: VEGF_Exosomes_Exosome_Counts.csv Description: Exosome concentrations quantified by tunable resistive pulse sensing. Variables: whole TCM: Exosome count in unfractionated tumor-conditioned media exo_rich: Exosome count in exosome-only fraction Ratio: Ratio of exosomes in whole TCM to exosome-only fraction File: VEGF_Exosomes_Exosome_depletion_experiment.csv Description: VEGF secretion from macrophages (n=3 donors) treated with fractionated tumor-conditioned media from 7 cell lines (21 conditions total: 7 lines × 3 fractions). Variables: Condition: Cell line letter (J=Jones, M=MacKinley, N=Nike, O2=OS2.4, O8=OSA8, P=Parks, S=STS-1) + donor number (1–3) + fraction (none=whole TCM, x=exosome-depleted, o=exosome-only) VEGF from Macs: VEGF concentration (pg/mL) File: VEGF_Exosomes_Measuring_VEGF_in_TCM_.csv Description: VEGF concentrations in tumor-conditioned media compared to VEGF secretion from macrophages (n=6 donors). Variables: cell_line: Cell line name VEGF in TCM: VEGF in tumor-conditioned media (pg/mL) 1–6: VEGF secreted by macrophages from each donor (pg/mL) File: VEGF_Exosomes_Lysed_Exosomes_.csv Description: Ratio of VEGF in lysed exosomes versus exosome-depleted tumor-conditioned media. Variables: HighMVB12A: Ratio in high-MVB12A expressing cell lines LowMVB12A: Ratio in low-MVB12A expressing cell lines File: VEGF_Exosomes_MVB12A_Expression.csv Description: VEGF secretion from macrophages (n=3 donors) treated with tumor-conditioned media from cell lines categorized by MVB12A expression. Variables: Cell Line: Cell line name Dog 1, 2, 3: VEGF secreted by macrophages from each donor (pg/mL) MVB12A: MVB12A expression status (high or low) Access information Analysis code is available on GitHub (https://github.com/rbrady783/TCM-macrophages). This Zenodo archive contains both the raw data and a snapshot of the analysis code.