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).<br>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.<br><b>Liu-et-al-Macrophage-Network-Model.zip</b><br>Code for logic-based differential equation model of the macrophage signaling network.<br><b>Supplementary Table S1.</b> 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.<br> <b>Supplementary Table S2.</b> 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.<br> <b>Supplementary Table S3.</b> 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.<br>