RNA-seq analysis of macrophages that are proximal or distal to tumor cells

To analyze the proximity-dependent gene expression in macrophages cocultured with tumor cells, we integrated QMID and RNA-seq to profile the transcriptome in THP1-derived macrophages cocultured with tumor cells. Overall design: THP1-derived macrophages cocultured with HER2+ MDA-MB-231 cells at a ratio of 20:1 and labeled via QMID, followed by FACS isolation and RNA-seq analysis. Proximial and distal macrophages were sorted out by measuring their QMID labeling intensities. Monocultured macrophages were set as control groups. All experiments were performed in triplicates.