Single cell RNAseq of mouse colon stroma during chronic DSS and homeostatic condition

We implemented a murine model of intestinal inflammation based on oral administration of multiple cycles of low dose dextran sulfate sodium (DSS) to induce epithelial injury and ECM deposition. Mice were subjected to 3 repetitive cycles of DSS displayed progressive accumulation of immune cell infiltrates associated with excessive deposition of collagen fibers. Lamina propria cells from water-fed and DSS-fed mice were isolated using enzymatic digestion, and enriched for stromal cells by FACS using antibodies excluding hematopoietic cells (CD45), epithelial cells (EpCAM), and erythrocytes. Prepared single cell suspensions were then profiled using the 10x Chromium V2 droplet-based single cell RNA sequencing platform. Tissues were collected from proximal and distal colon. A total of 3 female mice (12 weeks old) were processed for each treatment group and analyzed by single-cell RNA-seq. Female mice were utilized because they were able to withstand 3 cycles of DSS, whereas males exhibited morbidity.