The supplemental information provides detailed experimental procedures, data analysis, and supplementary figures for the study on transcriptome-based network analysis of human macrophage activation. It includes: 1. **Figure Legends to Figures S1-S5**: These figures illustrate the relationships between monocyte-derived macrophages (M^b) and other cell types, gene expression patterns associated with distinct stimuli, activation-specific genes revealed by Weighted Correlation Network Analysis (WGCNA), comparison of reverse engineering approaches, and permissive histone marks and PU.1 binding sites at major hub gene loci. 2. **Table Legends to Tables S1-S5**: These tables provide information on sample information, WGCNA modules, reverse engineering of regulatory networks, comparison of murine macrophage and dendritic cell signature genes, and abbreviations and descriptions of used algorithms and software. 3. **Supplemental Experimental Procedures**: Detailed protocols for isolating human blood-derived cells, generating and differentiating human macrophages, phenotypic analysis, ELISA detection, Western blot analysis, T-cell activation assays, RNA isolation, gene expression profiling, bioinformatics analysis, and reverse engineering of the core macrophage activation network. 4. **Common Transcription Factor Binding Site Prediction**: Methods for predicting common transcription factor binding sites using Genomatix Suite. 5. **miRNA-Seq Data Generation and Analysis**: Methods for miRNA sequencing, data normalization, and differential expression analysis. 6. **Histone Modification and TF ChIP-Seq Data Generation and Analysis**: Methods for native ChIP experiments to assess histone modifications and PU.1 binding, data normalization, and visualization of permissive histone marks and PU.1 binding sites. 7. **Link to Online Resource**: A web resource for the dataset of human macrophage activation, providing tables with normalized data, scripts, and additional information. This supplemental information supports the main findings and provides comprehensive details for reproducibility and further analysis.The supplemental information provides detailed experimental procedures, data analysis, and supplementary figures for the study on transcriptome-based network analysis of human macrophage activation. It includes: 1. **Figure Legends to Figures S1-S5**: These figures illustrate the relationships between monocyte-derived macrophages (M^b) and other cell types, gene expression patterns associated with distinct stimuli, activation-specific genes revealed by Weighted Correlation Network Analysis (WGCNA), comparison of reverse engineering approaches, and permissive histone marks and PU.1 binding sites at major hub gene loci. 2. **Table Legends to Tables S1-S5**: These tables provide information on sample information, WGCNA modules, reverse engineering of regulatory networks, comparison of murine macrophage and dendritic cell signature genes, and abbreviations and descriptions of used algorithms and software. 3. **Supplemental Experimental Procedures**: Detailed protocols for isolating human blood-derived cells, generating and differentiating human macrophages, phenotypic analysis, ELISA detection, Western blot analysis, T-cell activation assays, RNA isolation, gene expression profiling, bioinformatics analysis, and reverse engineering of the core macrophage activation network. 4. **Common Transcription Factor Binding Site Prediction**: Methods for predicting common transcription factor binding sites using Genomatix Suite. 5. **miRNA-Seq Data Generation and Analysis**: Methods for miRNA sequencing, data normalization, and differential expression analysis. 6. **Histone Modification and TF ChIP-Seq Data Generation and Analysis**: Methods for native ChIP experiments to assess histone modifications and PU.1 binding, data normalization, and visualization of permissive histone marks and PU.1 binding sites. 7. **Link to Online Resource**: A web resource for the dataset of human macrophage activation, providing tables with normalized data, scripts, and additional information. This supplemental information supports the main findings and provides comprehensive details for reproducibility and further analysis.