Liu-et-al-Macrophage-Network

Data and code from: Xiaji Liu1, Jingyuan Zhang1, Angela C. Zeigler1, Anders R. Nelson1, Merry L. Lindsey2, and Jeffrey J. Saucerman1* Network analysis reveals a distinct axis of macrophage activation in response to conflicting inflammatory cues. (Submitted).This repository provides the code and the necessary inputs used in the manuscript, along with simulation data and experimental data. Please refer to saucermanlab/Netflux for the LDE model generation.Liu-et-al-Macrophage-Network-Model.zipCode for logic-based differential equation model of the macrophage signaling network.Supplementary Table S1. Macrophage signaling network model. This spreadsheet contains the model network structure, parameters, and supporting literature references. This spreadsheet can be opened by Netflux for network simulations. Supplementary Table S2. Differential gene expression of peritoneal macrophages in response to LPS+IFNγ vs. untreated control. This spreadsheet contains the full DESeq differential gene expression analysis. Samples X8533M0_S1, X8534M0_S4, X8535M0_S7, and X8536M0_S10 are from untreated control. Samples X8533M1_S2, X8534M1_S5, X8535M1_S8, X8536M1_S11 are from LPS+IFNγ-treated cells. Supplementary Table S3. Differential gene expression of peritoneal macrophages in response to IL4 vs. untreated control. This spreadsheet contains the full DESeq2 differential gene expression analysis. Samples X8533M0_S1, X8534M0_S4, X8535M0_S7, and X8536M0_S10 are from untreated control. Samples X8533M2_S3, X8534M2_S6, X8535M2_S9, and X8536M2_S12 are from IL4-treated cells.