title: scRNA-seq of Mus musculus: 7days old small intestine
design: Single Epithelial cells were isolated and sorted from pooled small intestines (n=4) of 7 days old mice colonized from birth on with OMM9+E. coli DSM 112117. Cell sorting was performed on a FACS ARIA II (BD) equipped with a 100 mm nozzle and using the BD FACS DIVA 8.0.1 software. Live epithelial cells were further processed using the Chromium Next GEM Single Cell 3 Reagent Kits v3.1 according to manufacturers instruction (10x Genomics, Inc., United States). 10,000 single epithelial cells were aimed for sequencing. Single-cell sequencing on High-Output flow cells using 150 cycles was performed on an Illumina NextSeq 500 platform.